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Crimes Against Humanity in East Timor, January to October 1999: Their Nature and Causes

By James Dunn
14 February 2001 

I.       Executive Summary
II.      Introduction
III.     The aim and scope of the report
IV.     Some Relevant Historical Notes
V.      The Role of the Indonesian Military, the Formation of the Militia and the Campaign of Terror
VI.     The Crimes Against Humanity

VII.    The Major Crimes and the Killing Fields
VIII.   The Major Killings and their Characteristics
XI.     Responsibility for the Crimes Against Humanity
X.      The Commanders
XI.     Sources of Information and Acknowledgements

Annex A:      Senior Indonesian Military Officers Who Should Be Investigated Relation to Crimes Against Humanity in East Timor

Annex B:      Select Chronology

I. Executive Summary

1. The wave of so-called militia violence which swept over East Timor in 1999, culminating in massive deportations and destruction in September, was not the spontaneous response of those who favoured integration, but the outcome of a decision by TNI generals to counter the surge of popular support in East Timor for independence, by means of intimidation and violence, and to prevent the loss of the province to the Republic of Indonesia. The campaign of massive destruction, deportation and killings in September was essentially an operation planned and carried out by the TNI, with militia participation, to punish the people of East Timor for their vote against integration. 

2. While some of the pro-integrationists, in particular leaders such as Governor Abilio Soares, Joao Tavares and Eurico Guterres, may have enthusiastically welcomed the formation of the militia, and its operational agenda, most of the minority who favoured staying with Indonesia would not have resorted to violence in pursuit of their preference.

3. Several of the senior TNI officers mentioned in this report not only sponsored the setting up of the militia, provided training, arms, money and in some cases drugs, they also encouraged its campaign of violence, and organised the wave of destruction and deportation which occurred between 5 and 20 September. I share with the authors of Indonesia’s KPP HAM report the view that it is inconceivable that General Wiranto, then head of Indonesia’s armed forces, was not aware of the massive operation mounted by subordinate generals. The magnitude of the operation and the resources needed to conduct it, would have required at least his condonement, for it to have been carried out.  

4. The wave of violence led to very serious crimes against humanity. They include: killings, including mass murder, torture, abduction, sexual assault and assault against children, as well as mass deportation, and forced dislocation. The crimes against humanity also include the massive destruction of shelter, and of services essential to the upholding of the basic rights of the East Timorese to healthcare and education. In addition there was a massive theft of the property of the people of East Timor.

5. As the result of these crimes East Timor was left without an infrastructure, with its towns and villages in ruins. Its development was in effect set back more than a generation.  

6. With the continued forced detention of those East Timorese in refugee camps in West Timor who wish to return to their homeland, one of the most serious crimes against humanity being considered in this report, is in fact still being perpetrated.  

7. The failure so far of the Government of Indonesia to bring before a tribunal those responsible for the crimes committed in East Timor in 1999 is a matter of considerable disappointment. On the other hand, the efforts of those who compiled the KPP HAM report are to be congratulated for their commitment, their candour and their impartiality.


  1. Efforts should be stepped up to establish the guilt of those ultimately responsible, or with shared responsibility, for the crimes committed in 1999, and to commence action to have them brought to justice. Particular attention needs to be given to investigating the roles played by TNI commanders, with a view to laying charges against those responsible for the events of 1999. To meet these challenges, which carry sensitive political and diplomatic implications, structural changes should be made to the sections presently dealing with these matters, namely the Office of the General Prosecutor and the Serious Crimes Investigation Unit.
  2. The trials of those East Timorese militia at present in detention in Dili should be expedited. In judging their cases careful consideration needs to be given to the impact of the militia/TNI command structure on their actions, and to the factor of shared guilt.
  3. In the event that no progress is made in Indonesia towards bringing to justice those responsible for the crimes committed in East Timor in 1999, immediate steps should be taken to negotiate the setting up of and international tribunal for this purpose.
  4. The question of reparations, or some form of compensation, in relation to the massive destruction of shelter and buildings functioning for the well-being of the people, as well as the extensive and organised theft of property, should be placed prominently on the agenda, in relation to negotiations with the Government of Indonesia.
  5. A solution to the position of East Timorese refugees in West Timor is a matter of considerable importance, since those detained against their will remain victims of a serious crime. Therefore, the efforts of UNTAET’s Transitional Administrator and UNHCR to resolve this issue deserve stronger support from the international community.
  6. While this report focuses on events in 1999, in the course of my enquiries persistent allegations of very serious crimes against humanity, involving mass murder, since East Timor was invaded in 1975 have been brought to my attention. I join with the KPP HAM report (recommendation 27) in calling for a thorough investigation of what transpired and of who was responsible. The most serious crimes, such as the Creras and Santa Cruz massacres, are crimes of such magnitude that they must be considered of concern to the international community as a whole. 
  7. Action in relation to these matters is important both to the fulfillment of UNTAET’s mandate in East Timor, and to the development of an appropriately harmonious relationship between the new nation and Indonesia.

James Dunn, Dili
14 February 2001

II.          Introduction

The actions violating human rights and international humanitarian law in East Timor were directed against a decision of the United Nations Security Council, acting under Chapter VII of the Charter, and were contrary to agreements reached by Indonesia with the United Nations to carry out that Security Council decision. Under Article 25 of the Charter, Member States agree to accept and carry out the decisions of the Security Council. The organized opposition in East Timor to the Security decision requires specific international attention and response. The United Nations, as an organization, has a vested interest in participating in the entire process of investigation, establishing responsibility and punishing those responsible and in promoting reconciliation. Effectively dealing with this issue will be important for ensuring that future Security Council decisions are respected. (Para 147, ICI Report)

In October last year I was invited by Mr Mohamed Othman, the Prosecutor General to accept a commission to prepare a general report on the events behind the crimes against humanity committed in East Timor in 1999, and their background, to assist the Court in its deliberation of the crimes against humanity cases that would be coming before it. I also saw this request as an opportunity to compile a report for a wider readership, in particular for those in the United Nations system with an interest, even a passing one, in the world body’s role in guiding the new nation from the ashes and chaos of October 1999 to full eventual independence. I have attempted to present this report in a form suitable to the court, but it must remain essentially the presentation of an experienced observer of the recent history of East Timor, without the legal precision and definitive substantiation which marks the discipline of prosecuting lawyers in their handling of individual cases. I hope this report will serve as a modest aid both to the Court and to others with an interest in the tragic events that transpired in East Timor in 1999. The thrust of the report, therefore, is to explain and analyse, rather that to present the case for the prosecution. As it turned out, with extremely limited assistance this modest effort has in fact been a marathon task, and no doubt some aspects of what is a rather complex pattern of events will not have been adequately treated.

III.    The aim and scope of the report

1. This report is essentially a general examination of what I believe to be the main elements behind the tragic and disastrous events which swept over East Timor in 1999. Its aim is to improve the understanding of United Nations officials charged with responsibility for the investigation and eventual prosecution of crimes against humanity which, it is alleged, were perpetrated against the people of East Timor by the armed forces of Indonesia and the militia between 1 January and 25 October 1999. In preparing this report I have taken into account the findings and conclusions of the report of the International Commission of Inquiry established in November 1999 by CHR Resolution 1999/.S-4/1 of 27 September 1999, and endorsed by ECOSOC decision 1999/293 of 15 November 1999.[1]I have also taken careful account of the commendable efforts by Indonesia’s KPP HAM to investigate these crimes against humanity, to identify those responsible for them, and to bring them to justice.[2]This report is frank and detailed, and its conclusions reflect the commitment, the impartiality and the concern of its authors.

2. The ICI report, referred to, recommended that its conclusions be considered a ‘starting point in the process of bringing those responsible to justice’. It expressed “the view that ultimately the Indonesian Army was responsible for the intimidation, terror, killings, and other acts of violence experienced by the people of East Timor before and after the popular consultation.”[3] In this report I have set out to, among other things, assist further progress in that direction, by showing that there is evidence available - much of which I have been unable to present in detail in the limited time available and with the extremely limited resources available - to justify the institution of proceedings against certain senior officers of the Indonesian National Army (the TNI), as well as leaders and members of the militia, in relation to the counts of crimes against humanity that were highlighted in the ICI report. Already, it is noted, the Government of Indonesia has announced its intention to bring some, but not all, of the persons mentioned in this report, before a Tribunal in Jakarta, an undertaking that has yet to be fulfilled.

3. Because those who planned and facilitated militia operations, including most militia group leaders, are now in Indonesia, the institution of these proceedings and, where appropriate, prosecution, involves complex international negotiations if this fundamentally important exercise in upholding international humanitarian law and human rights is to succeed. While the prosecution of members of militia units who are held in East Timor is an encouraging beginning, the fact that those who organised, trained and directed their operations are still inaccessible to UNTAET’s law-enforcement agencies will present a moral dilemma until the problem of access is resolved.

In dealing with individual cases of militia killings here in Dili, where the accused is charged with murder, it is important to take account of the wider context - what we call crimes against humanity. These crimes were planned and are systematic in character. The victim was only one of many, and the aim was to intimidate, terrorize, eliminate or punish a target group of persons. In most of these cases responsibility for the crime must, at least, be shared between the killer and those who planned or made possible the operation in which the crime was committed. Acknowledging the command responsibility is central to the pursuit of justice in relation to war crimes, or what we call crimes against humanity. In the case of the events that occurred in 1999 it follows that the ultimate responsibility rests with those who planned, organised, trained and equipped the militia. It is also apparent that the brutal TNI culture, which led to serious human rights violations from December 1975 onwards, left its imprint on the various incidents in 1999. My own research into events of that time has revealed a consistent pattern of brutality, in the TNI’s response to opposition to the integration of East Timor into Indonesia. In the wider perspective, it is worth recalling the recommendation contained the report of Mr Bacre Waly Ndiaye, Special Rapporteur, on his mission to East Timor in July 1994. In relation to the Santa Cruz killings, he stated that these

“killings should not be considered as a thing of the past. They must not be forgotten, and there is still time to correct the shortcomings, noted at all levels, in the way in which violations of the right to life have been dealt with by the Indonesian authorities in East Timor: it is not too late to conduct proper investigations, to identify and bring to justice the perpetrators, to determine the fate and whereabouts of the missing persons, to grant compensation to the victims or their relatives, and to prevent the occurrence of further killings.”[4]

4. The further pursuit of justice in this matter is dependent on political cooperation from the Government of Indonesia. While the early responses from the Government of President Wahid have been encouraging, the political climate in Indonesia may have changed to the extent that the further pursuit of these matters could well turn out to be a lengthy process, with their ultimate resolution being dependent on the support and political will of the international community. The record so far is bleak. As Professor Harold Crouch, a leading international authority on Indonesian politics, states in a recent report (in relation to legal action in Indonesia in general) that: “Although the investigations (so far) have uncovered much evidence of killing and other crimes, they have not produced more than a handful of prosecutions. And even when convictions have been obtained, the sentences have often been extraordinarily light, and suspected ‘masterminds’ behind the offences have not been charged.”[5] However, the major crimes against humanity that were committed in East Timor in 1999, in fact those committed since the beginning of the Indonesian occupation of Timor Loro’sae, cannot be left to drift into historical obscurity. In terms of their magnitude and the brutality attending them, these incidents are extremely serious crimes, by any measure, and should therefore be addressed by the international community, at the very least in the event that, for whatever political reasons, the authorities of Indonesia are unable, or even disinclined, to confront them. The option of the setting up of an international tribunal will need to be considered, in order to deal with those responsible for the crimes against humanity in East Timor during a period when the welfare of the people of this country was formally considered by the United Nations not to be the legitimate property of the Indonesian authorities. The challenge before the international community has been succinctly recorded by Harold Crouch:

The international community will lose its credibility if it ceases to insist on trials of gross human rights offenders where Indonesia has undertaken its most visible obligation, namely with respect to events in East Timor in 1999. But more than credibility is involved. At bottom the international community’s continued involvement with the accountability issue is grounded in a belief that its own interests are deeply involved in Indonesia’s efforts to establish a stable and secure democratic society since Indonesia is one of the world’s most populous and significant countries.[6]

5. Between 1 January and 25 October 1999 widespread extra judicial, summary or arbitrary executions, including both mass murder, and individual killings, as well as torture and violence against women, were carried out against the people of East Timor. These crimes against humanity were planned, were systematically carried out, and were perpetrated on a wide scale. They were directed against particular groups; in particular, leaders of the independence movement and East Timorese who were perceived to be their supporters, but these actions often degenerated into indiscriminate killings. In some cases brutal attacks were also directed against Church officials on the grounds, that the Church was perceived as supporting the option of independence. Apart from killings, these attacks on the person led to widespread injuries, to sexual assaults against women, and to abductions.

6. Activities by the militia and the TNI, in September 1999, led to the widespread massive displacement and deportation of peoples. The evidence, based on a wide sampling of interviews and on the observations of other observers, indicates that most East Timorese transported to West Timor were in fact forced to go against their will. They were given orders or explicit directions, often accompanied by threats of violence. Also it was the well-founded fear of violence from TNI/militia forces that caused tens of thousands of East Timorese to flee from their homes to mountain areas, where they were to endure food shortages, lack of medical treatment, and other difficulties until international relief arrived, and the security of their home environments was ensured by the presence of Interfet forces. In total more than 500,000 Timorese, or more than 60% of the entire population, were displaced by the violence or threats of violence in September 1999. Moreover, the entire administrative and social order of the province was destroyed so that in November 1999, when UNTAET was first established, the returning East Timorese were assembling in devastated towns and villages totally devoid of the basic infrastructure of a community.

IV.     Some Relevant Historical Notes

7. The island of Timor came under Portuguese influence in the first half of the sixteenth century, when the Portuguese established a colony in the Solor Islands, east of Flores. The Portuguese presence in Oecussi was established in the seventeenth century, but it was not until 1769 that the serious colonization of what is now East Timor was begun, when the Portuguese colonial administration was moved to Dili. The present division of the island was agreed to in general terms in the mid-nineteenth century, but was not confirmed until the Sentenca Arbitral agreement of 1913. Portuguese colonial rule continued unchallenged until an intervention by Allied forces in late 1941 led to an occupation by Japan until the latter surrendered in August 1945. Portugal was then able to resume its colonial rule.

8. Soon after Indonesia gained its independence in 1949, the Sukarno government lodged a claim to the adjacent territory of Dutch West New Guinea, which it eventually formally acquired in 1979, but at no stage did the Government of Indonesia lay a claim to Portuguese East Timor. Following the Lisbon Coup in April 1974, the people of East Timor, along with the peoples of other Portuguese colonies, were extended by the new Portuguese government the right to determine their own future, and choose independence if they so wished. Early in 1975 the two major parties, UDT and Fretilin, formed a coalition for independence, a rather flimsy arrangement which failed to survive in the face of an Indonesian intelligence strategy designed to bring about its collapse. Thanks in part to these efforts the Portuguese colonial administration’s a decolonisation programme was hampered by a widening gulf between the two major parties.

9. The next move by Indonesian intelligence was to provoke a brief civil conflict between the Fretilin and UDT parties. However, in October 1975, a month after the Fretilin victory over its rival, Indonesian forces entered the province in a covert military operation, which was designed ultimately to bring about the integration of the colony. This invasion was, in the event, strongly resisted by the forces of Fretilin, at the time the de facto administration of the territory, which was seeking the return of the Portuguese (who had retired to Atauro), and the resumption of the decolonisation programme. The major invasion of East Timor then took place on 7 December 1975.

10. In a strongly worded UN General Assembly Resolution Indonesia was called on to withdraw its troops from the territory and to allow for a genuine act of self-determination. The General Assembly also referred the matter to the Security Council, which repeated the demand that Indonesian withdraw its troops. The Government of Indonesia did not comply with these demands and, largely because of an extremely low level of interest on the part of the major players in the international community, the Security Council Resolution appeared to wither on the vine. In July 1976, in disregard of the concerns of the United Nations, President Suharto proclaimed East Timor the 27th province of the Republic. This action was not, however, recognized by the United Nations, the status of East Timor remaining on its agenda as an unresolved issue until the dramatic events of 1999. UNGA Resolution 30/37 of 1982 set the stage for a process of negotiation between the representatives of Portugal and Indonesia, a process that proceeded only fitfully until after the Santa Cruz massacre of 1991.

11. In the meantime, the people of East Timor suffered tragically as Indonesia resorted to severe military measures in order to suppress persistent opposition to the illegal integration of the territory. As a background to the events of 1999 it is important that the pattern of violations against the people of East Timor should be taken into account. From the very beginning of the military intervention, there were persistent reports of gross human rights violations. In the week following the invasion of Dili hundreds of citizens of the capital, almost all of them non-combatants, were summarily executed. These killings, some of which took the form of mass executions, included women and at least one foreigner, Roger East, a journalist from Australia. Mass executions at Liquiça, Maubara, Aileu and near Bobonaro were reported in the months following the invasion. According to reports received in Australia from Church sources, as many as 60,000 Timorese may have died in the year following the invasion, and as many as 200,000 in the subsequent four years, many of course from disease and starvation. Summary executions continued in the eighties and nineties, the worst known cases being the Creras massacres, where more than 1,000 East Timorese were killed by rampaging TNI troops, and the Santa Cruz massacre, which reportedly claimed the lives of more than 200 Timorese. There were also persistent reports of torture and sexual assault, which were given frequent attention in the annual [7]reports of Amnesty International and, later, Human Rights Watch. However, until the Santa Cruz incident the response from the international community was negligible, with the major powers declining to support the few calls for an international investigation.

12. It is important that this pattern of behaviour on the part of the Indonesian military be taken into account when judging the events of 1999. The relevance of the historical background was noted in the KPP HAM report, which recommended that “a comprehensive investigation be carried out into all crimes against humanity committed in East Timor since 1975”.[8] TNI attitudes during this period clearly[9] reflected a persistent disregard for basic human rights, especially when dealing with those suspected of being opposed to integration. The military’s persistent brutal treatment of the East Timorese, including the mass killings, was evidently ignored or tolerated by the Government of Indonesia, a stance no doubt encouraged by the extremely low level of interest in the plight of the people of this remote and, at that time, little-known territory. There was, however, considerable international reaction to the Santa Cruz killings, but summary executions on a smaller scale, torture and other abuse in fact continued. As recently as 1995 six East Timorese were executed in the Liquiça area, although in this case a TNI officer was charged with the offense. From the outcome of these trials it was evident that the Suharto Government had not address what had become a culture of oppression and brutality in East Timor.

13. In January of that year President Habibie agreed to allow the people of East Timor to decide between the option of autonomy and independence. Arrangements for the plebiscite were agreed to on 5 May, with UNAMET undertaking the task of setting up the plebiscite. [10]The vote was taken on 30 August and on 4 September the results were announced. 78.5% of a voting turnout of more than 98%, came out against the autonomy proposal.

14. Militia violence against supporters of independence began early in 1999, and in earnest in April when Operasi Sapu jagad (Operation Clean Sweep)[11] was launched. However, the main thrust of the violence occurred between 4th September, when the results of the plebiscite were announced in Dili, and the end of September, when the INTERFET force was able to restore security to the central and eastern sectors of East Timor. This operation of massive destruction, ransacking and deportation was also devised by the TNI when it was realised that the plebiscite was likely to go against integration. Accordingly, in July the TNI began developing Operasi Wiradharma, the evacuation of East Timor, an operation which apparently also used the code-name, Guntur. The plan, which was devised at least two months before it was launched, was commanded by TNI Kopassus officers, with Major Generals Zakky Anwar Makarim and Adam Damiri playing key command roles. According to informed sources in Jakarta, it was planned to deport most of East Timor’s population to West Timor, from where they would later be dispersed to other parts of the archipelago. The planners seemed to believe that the violence would persuade the MPR, the Indonesian Parliament, to reject the outcome of the ballot. The operation began in the immediate aftermath of the announcing of the results of the plebiscite, and was focused on the deportation of a large part of the population of East Timor, the destruction of most houses and buildings, and on a campaign of terror against the staff of UNAMET, foreign journalists and other foreigners present in East Timor at that time.

V.      The Role of the Indonesian Military, the Formation of the Militia and the Campaign of Terror

15. The use of the term ‘militia’ may be of recent origin in East Timor, but the training and use of Timorese in para-military units goes back to the time of Indonesia’s military intervention in East Timor in 1975. In that year the oldest of the militia units, Halilintar, was established following a covert military training program conducted in West Timor by a special TNI military force, commanded by then Colonel Dading Kalbuardi. [12] This operation was code-named Operasi Komodo, and its aim was to procure the integration of Portuguese Timor, which was then in the process of decolonisation. Halilintar troops, then led by Tomas Gonçalves and Joao Tavares, accompanied the TNI military force in a support capacity, in Operasi Flamboyan (Operation Poinciana tree), a covert military action against Fretilin forces in West Timor in mid-October 1975 in the aftermath of the latter’s victory over UDT. It was an operation planned by the then commanders of RPKAD (the Army Paratroop Regiment) and members of OPSUS (special operations), an elite combination which was the pre-cursor of Kopassus, ABRI’s Special Forces command. The way East Timorese were used in this operation marked the beginning of a TNI policy of using willing Timorese in operations conceived and planned by military commanders, in which the former provided a political front designed to mask the leading role of the Indonesian military.

16. In 1976, some months after the invasion of Dili, most of the Halilintar troops were re-deployed to form the basis of Battalion 744,[13] a regular territorial unit, which was later to be joined by Battalion 745. These units were largely made up of Timorese soldiers, but were staffed by Indonesian officers. Halilintar itself was disbanded in 1982, and was not reformed until 1998. In the late seventies Timorese were again used in paramilitary roles in the Hansip, or civil defence units, which in fact also existed in other parts of Indonesia. The development of these bodies took place against the background of a harsh, and at times brutal, campaign against the population of East Timor by the occupying military forces. While considerable international attention has been devoted to the killing of five newsmen from Australia at Balibo in October 1975, this incident was only the first of a serious of atrocities alleged to have been committed by Indonesian military units over the ensuing 16 years. Summary executions on a mass scale began in the days following the invasion of Dili on 7 December, when hundreds of East Timorese were killed, many of them in several mass executions. Similar atrocities were reported elsewhere in Timor in the next three years, during a period when there were no international observers in the territory to bear witness to these incidents of summary execution and indiscriminate killing.

17. Thus mass killings were reported (mostly by Church sources) to have occurred at several locations, mostly in the interior of the island. One of the most serious of these tragic incidents, which was said to have claimed the lives of more than 1,200 East Timorese, was reported to have occurred near Bobonaro in 1976. [14]Later, in 1983, according to a Timorese official who investigated the incident, more than 1000 Timorese were killed in the Ossu area by rampaging Indonesian troops. The massacre was in revenge for the earlier killing of 16 TNI troops by Falintil guerrillas, which itself was a response to the brutal rape of a Timorese woman by TNI troops. The fact that these tragic events led to no action by the Indonesian authorities to discipline the units concerned, or pressured from the international community, appears to have created a conviction among the military commanders concerned that they enjoyed an immunity from legal action or international scrutiny. The TNI’s culture of oppression and brutality, which has already been referred to, had been formally established. Until 1999 the only major incident to attract significant international attention was the massacre of more than 200 Timorese by Indonesian troops, following a peaceful demonstration at Santa Cruz cemetery in November 1991. In the face of international pressures some legal action was taken against a small number of troops. However, it is noteworthy that they were accused not of murder but of having disobeyed orders. Their sentences were light, and stood in stark contrast to the heavy prison sentences handed down to several Timorese demonstrators by an Indonesian court. While this incident caused international concern and some action by the United Nations, the response was hardly enough to end what had become, during the Suharto regime, standard practice in the way the Indonesian military treated dissidents, whether in East Timor or elsewhere in the Republic.

18. It is against this background that the setting up of the militia and the way it resorted to brutal tactics need to be considered. The origins of Timorese para-military units have already been examined. The militia as it existed in 1999, and as an extension of the para-military force Halilintar, go back to the eighties when East Timorese para-military units were again formed, specifically to involve the local population in operations not only against Falintil, the armed resistance, but against the growing phenomenon of passive resistance. The best known of these early units was Team Alpha (Tim Alfa) which, with Team Saka (Tim Saka), was formed in 1986 in the eastern sector of East Timor by a Kopassus officer, Captain Luhud Pandjaitan, reportedly acting on orders from his commander, then Colonel Prabowo. Team Alpha’s members were trained and paid, and their operations against pro-independence elements organised, by Indonesian military officers. Another significant move was the setting up of the Gada Paksi (Gadu Penegak Integrasi – Guards to Uphold Integration) in 1994, also reportedly by Prabowo. The Gada Paksi was conceived as a way of mobilizing young pro-integration activists.

19. The formation of the militia was evidently yet another initiative of Kopassus, the TNI’s Special Forces Command. This special military group became a select army within Indonesia’s military force structure, at the time called ABRI (Armed Forces of the Republic of Indonesia). Its members were specially chosen, received special training and equipment, enjoyed privileges and were generally regarded as an elite corps, with, in the time of President Suharto, the elite mission of protecting the integrity of the Indonesian state. While elements of Kopassus (Groups 1 and 2) made up a special combat force, other parts of the force have been engaged in operations of a covert kind. Hence, Group 3 was said to have dealt with terrorism, while Groups 4 and 5 have in the past been engaged in intelligence operations against opposition groups, their actions included kidnapping and ‘disappearances’. The financing of the covert operations of this internal security force had reportedly been facilitated in part though the extensive business operations of Kopassus.[15]

20. Kopassus has had a long involvement in East Timor, its founding commanders having played key roles in the illegal military intervention against the Fretilin Administration in October 1975. Throughout the 24 years of Indonesian rule in East Timor, Kopassus officers have played a key role not only against the Falintil armed resistance, but also in the wider community against the growing ranks of Timorese pro-independence activists. Events in the months following the downfall of President Suharto became a matter of some concern to TNI officers in East Timor, where Kopassus members occupied key posts. Moves by President Habibie to dismantle the so-called Orde Baru, and liberalise Indonesian politics, served to stimulate demands in East Timor for the right to self-determination the people of the territory had not yet been able to exercise.

21. Based on the material I have been able to examine it is clear that the setting up of the militia, in the form it assumed in 1999, was the outcome, not of pro-integrationist Timorese demands, but of an initiative by a group of senior TNI officers, all of whom appear to have been members of Kopassus. These officers were motivated by a determination to head off the risk of losing East Timor as a consequence of mounting domestic pressures on President Habibie, including pressures for democratic reform, international urgings and increased United Nations efforts. Statements by the President himself, in the months following his appointment, foreshadowed a significant change of policy on the part of the new government of Indonesia. On 9 June 1998 President Habibie told a Reuters correspondent that he was considering “special status” and wider autonomy to East Timor. Less than a week later 1500 East Timorese students demonstrated in Dili, where they called for a referendum and for the release of Xanana Gusmão. On 18 June Foreign Minister Ali Alatas presented new proposals to Portugal regarding East Timor. These events led to more public protests, with violent responses from Indonesian troops, who killed several student demonstrators.

22. The plan to develop the militia in all districts of the province of East Timor may have enjoyed the support of leading Timorese opposed to change – among them, Governor Abilio Soares, Francisco Lopes da Cruz and Joao Tavares, but it was initially a military response, a plan devised by Generals Syamsuddin and Zakky Anwar Makarim, between July and September 1998.[16] According to the testimony of Julio Fernandes, the official launch of the militia occurred on 10 or 12 August 1998 at a meeting attended by Major General Damiri and Colonel Tono Suratman, as well as Joao Tavares, Eurico Guterres, and Cancio de Carvalho. Damiri and Suratman told those present that they must organise to protect integration.

23. At the time it was apparent that support for ultimate independence had grown rapidly in East Timor in the previous months. The formation of the militia was apparently perceived as a way of creating what in fact was an illusion - that the people of East Timor did not want independence, and were prepared to use coercion and even force in order to ensure that the province remained as a constituent part of the Indonesian Republic. Their views were of course shared by Timorese opposed to independence, such as the Governor, Abilio Soares, and other Timorese supporters of integration, from whose ranks leaders of the militia groups were chosen. On the other hand, as militia violence began to develop, some members became disillusioned and withdrew, while it became increasingly difficult to recruit new members. In the months leading up to the September violence, in some areas Militia leaders resorted to forms of conscription of new members, with violence being used on occasion against those who resisted.[17]

The organizational structure of the militia was virtually integrated into the TNI structure in East Timor.[18] Militia units were formed in each of the 13 Kabupaten (districts), with the commanders being chosen or confirmed by the TNI command. These were as follows:

1. Tim Alfa Lautem Leader: Joni Marques
2. Saka/Sera   Baucau   Serka Kopassus Joanico da Costa[19]
3. Pedjuang 59-75 Makikit  Viqueque    Martinho Fernandes
4. Ablai   Manufahi Nazario Corterel
5. AHI Aileu  Horacio
6. Mahidi   Ainaro    Cancio de Carvalho
7. Laksaur  Covalima Olivio Mendonca Moruk
8. Aitarak  Dili  Eurico Guterres
9. Sakunar Oecussi Simão Lopes
10. BMP (Besi Merah Putih)  Liquiça Manuel de Sousa
11. Halilintar
Joao de Tavares
Natalino Monteiro
12. Jati Merah Putih Lospalos Edmundo de Conceição Silva
13. Darah Merah Integrasi  Ermera   Lafaek Saburai


24. The above list is by no means an exhaustive one. In the Bobonaro/Maliana area, for example, there were at least six groups, with Halilintar forming the headquarters. While the plan to form these units was conceived and commenced in 1998, most were not operational until April 1999. These units varied in size, the most prominent being Halilintar and Aitarak. Halilintar’s commander, Joao Tavares, a former Bupati of Bobonaro district, was appointed Panglima, or overall commander of militia chiefs in East Timor, an appointment said to have been made by TNI officers. Tavares had had a long association with para-military bodies, having been a founder member of the Halilintar force, which accompanied Colonel Dading Kalbuardi’s RPKAD force on the TNI’s first major military assault against East Timor in October 1975.[20]

25. Aitarak came under the command of the flambouyant East Timorese, Eurico Guterres. A much younger man, Eurico’s earlier links had been with Fretilin. His parents had been killed by Indonesian troops, while he himself, when a teenager, had worked as a courier for Falintil before being captured by a Kopassus unit, which appears to have been responsible for the redirection of his loyalties.

VI.     The Crimes Against Humanity

26. The crimes against humanity committed in East Timor in 1999 are wide-ranging in their detail. They are outlined in greater detail elsewhere in this report. They are listed below, in rather general terms. As for the victims, while the main targets were pro-independence activists, and other known supporters of the independence movement, most of the people of the East Timorese nation virtually became victims of at least one of these crimes – e.g. deportation or deprivation of shelter. In September 1999 the priests, brothers and nuns became targets, not only because pro-independence supporters sought sanctuary in the churches, but because the Church was seen by at least some of the TNI commanders and militia leaders as being opposed to the autonomy option. These attitudes were manifestly present during the brutal killings at Suai and in Lautem, and the assault on Bishop Belo’s residence in Dili.

27. While it could not be said that these killings were of a genocidal character, there was a degree of wanton discrimination against families of the key targets, including women and children. East Timorese who had worked for UNAMET were also singled out, and in some cases were brutally executed. Indonesian nationals supporting the Timorese right to choose independence if they so wished, were also at risk and a number of them were lucky to escape with their lives.

VII.   The Major Crimes and the Killing Fields

28. In summary the following violations represented a massive onslaught on the human rights and well-being of the people of East Timor.

a. The wanton killing of hundreds of East Timorese. The true figure for the total loss of life is not yet known, and may never be known. However, on the basis of the information available, and on discussions with Church officials, Timorese human rights activists, Civpol and Interfet officers, and on my own observations in the period around the plebiscite it may well be greatly in excess of 1,000 persons. I gained the strong impression that not enough is known about killings outside the major atrocities, especially during the period between the announcement of the results of the plebiscite and the end of September. It is important to note that these killings were systematic, and were directed against the opponents of continued integration with Indonesia. When the violent acts occurred the situation was invariably one-sided, with the victims being unarmed, and unprotected by local law-enforcement authorities. The killings were often brutally carried out, with the bodies sometimes being mutilated.

b.      Hundreds of cases of injury to the person: In the period between early April and the end of September 1999, many Timorese were injured in militia attacks, especially in the Cova Lima, Bobonaro, Ermera, Liquiça and Dili areas.

c.       Many cases of torture, intimidation, rape and abduction: Many victims were beaten, some being left with serious injuries. There were also many assaults against women and children. According to a FOKUPERS report there were 182 cases of gender-based human rights violations. [21] These include rape, kidnapping and, in some instances, slavery.

d.      Forced deportation: It is generally accepted that more than 250,000 East Timorese were transported to Indonesia, most to West Timor. In almost all instances, according to my own enquiries, the Timorese were ordered, not requested or persuaded, to leave their homes. There are persistent reports from refugee camps in West Timor that the use of force has continued to be used to prevent those refugees who desire to return to their villages from doing so.

e.      The forced flight from their homes: More than 200,000 East Timorese were compelled, through what should be considered well-founded fears, to flee to the mountains. They were soon to be facing starvation in the conditions of the time. It should be noted that the flight to the mountainous interior occurred during the dry season when there was very little food to be found in the natural environment, especially in the hinterland of Dili.

f.        The willful destruction, damaging and ransacking of the houses or shelter: This massive scorched earth campaign caused the destruction of the basic shelter of more than 80% of East Timor’s population. In the urban areas at least, ransacking and pillaging denied tens of thousands of East Timorese of their worldly possessions. There was no subsequent attempt by the Indonesian authorities to organise the return of these goods.

g.      The willful destruction, ransacking or damaging of schools, health centres, etc.: The right to education and health are today widely considered fundamental rights. The destruction of these facilities has in effect severely set back these services in East Timor, especially in the field of education.

VIII.  The Major Killings and their Characteristics

29. Mass killings or executions have a understandably special quality of horror about them, and for that reason the main focus in East Timor has tended to be on the horrific killings in Suai, Liquiça, Maliana and other places. It needs to be stressed, however, that numerous killings on a smaller scale – often involving individuals – occurred elsewhere in the territory, and have attracted much less attention, including, I suspect, from UN investigators. These lesser-known killings and cases of assault on the person were part of the wave of brutalities carried out by the militia and the TNI. It reached most parts of East Timor, although there were great variations in intensity. Among the worst areas were Covalima and Suai and the Bobonaro/Maliana district. There were many individual killings, but they should be considered as part of the crimes against humanity, in that they were directed against individuals as members of a particular group, within the context of the wider aim of eliminating, neutralizing, or punishing the opposition to integration. The main wave of violence occurred in September, when many pro-independence supporters were singled out for summary execution while the systematically executed pembumihangusan, or scorched earth operation, was in progress.

29. In some instances, especially in the interior of the territory, these killings may have escaped investigation. Even in Dili, though my enquiries have hardly been exhaustive, I have not been able to establish just how many Timorese were killed in the rampage between 4 September and the arrival of Interfet. My investigations have produced a wide range of estimates – from 37 to what seems to be an improbable figure of 500, in the period under review. In Liquiça a figure of more than 200 was mentioned repeatedly by local residents. The large-scale killings, however, deserve special attention for a number of reasons. They required a degree of organization, and in most cases there was a visible, if not commanding, TNI participation, together with, at best, a total failure of the Polri to intervene to protect the citizens under attack, who were almost invariably unarmed. Throughout most of 1999 the armed resistance forces, the FALINTIL, were inactive, in response to specific orders from the Commander, and were in most cases unable to help protect their supporters. With some 18,000 TNI troops, and perhaps 20,000 militia in East Timor the FALINTIL force of less than 2,000 was massively outnumbered. Any attempt to intervene risked a massive reprisal against the civilian population. This was demonstrated at Cailaco, in the Maliana district on 12 April, when a FALINTIL-linked force killed Manuel Soares Gama and two TNI personnel, following the latter’s murder of six Timorese in Gama’s house. The very next day a force led by Lieutenant Colonel Siagian and Joao Tavares reportedly kidnapped, tortured and then executed six residents of Cailaco.

Killings in the Dili Area

30. The killing of Manuelito, the young son of Manuel Carrascalão, and at least 11 displaced Timorese from Liquiça, Alas and Turiscai, took place on 17 April 1999 at the Carrascalão residence in Dili, which was also used as the secretariat of the Movement for the Reconciliation and Unity of the People of East Timor, of which Manuel Carrascalão was Chairman. Manuelito’s companions and many refugees had sought refuge in the house from violence in their home towns. The house was attacked by Aitarak and Besi Merah Putih militia following a rally that day by more than 5,000 militia, outside the Governor’s office, a meeting that was presided over by Colonel Tono Suratman, the Korem commander. The attack was a particularly brutal one, on a house where there were some 143 persons seeking refuge. It took the life of Manuelito, the courageous teen-age son of Manuel, who attempted to persuade the militia to stop their assault and spare the lives of the refugees inside the house.

31. Some killings were reported in the following months, but the presence of UNAMET headquarters and a sizeable international community seems to have deterred the militia from further massacres, that is until the destructive assault of September. As the Aitarak militia grew in size and aggressiveness, violence began to increase, especially in August. On 5 September, the day following the release of the results of the plebiscite 25 people were reported to have been killed by Aitarak members at the Camara Ecclesiastica Diocese in Dili. On the following day some of the refugees in Bishop Belo’s house are reported to have been murdered, though the figures have not yet been confirmed. Some East Timorese university students who had just returned from Java, were also reported to have been killed. Others, including a German priest and a civilian, were killed in the period prior to the arrival of the Interfet forces, but the full casualties during this chaotic period are apparently still not known. The claim that bodies were taken out to sea in barges and disposed of has not been proven, but it cannot yet be dismissed. I was in Dili at the time, and was informed by a Timorese that this form of disposal was taking place, and myself witnessed two barges going far out into the waters between Dili and Atauro. They spent less than an hour in that location before returning to Dili. Based on my own observations, as well as reports from Timorese, the assault on Dili, which began on 4 September, less than two hours after the announcement of the plebiscite results, was led by TNI personnel, most of whom were dressed in Aitarak shirts. At the Bishop’s house an unnamed TNI Lieutenant Colonel escorted the Bishop away from the scene before the house was burned and several refugees killed.

The Oecussi Killings

32. While there were reports of murders and intimidation in the Oecussi enclave before August 1999, the main killings occurred on the 8th, 9th, and 10th September. The killers included members of 745 Battalion of the TNI and a substantial number of militia. On Wednesday 8 September a force, including about 200 troops attacked the villages of Tumin, Kiobiselo, Nonkikan and Nibin, and killed about 14 men. The next day at Imbate about 70 young men, who were said to have been selected on the basis of their educational ability, were separated from the rest of the people gathered there. They were bound in pairs and were marched to Passabe. At 1 am on 10 September, following a pre-arranged signal a mass slaughter of these young men was carried out, the victims being shot or hacked to death. According to the investigators, the main instigators of the massacre included the Police Chief of Passabe, Gabriel Colo, and Laurentino Soares, aka Moko, but it is also recorded that the massacre was controlled by a small number of men who were both TNI soldiers and members of the militia. The total number of victims is estimated at more than 70, but these killings could not be investigated until after the arrival of Interfet forces on 2 October. In the words of the investigator ‘there is no positive data available at this time to positively identify how many murders had occurred in the enclave between 1 January and 25 October 1999’. However the killings referred to above were said to be carried out ‘predominantly by the Sakunar Militia group, supported by the TNI.

Suai/Cova Lima:

33. The Cova Lima district, or kabupaten, in which Suai is located, was one of the worst centres of violence by the militia/TNI in 1999. Several independence supporters were killed in January, most of them by the Mahidi, in at least one case in an operation with infantry and Kopassus troops. The main atrocity occurred at the Ave Maria Church when at least 200 of displaced East Timorese who were seeking refuge there were slaughtered in an attack by Mahidin and Laksaur militia, supported by TNI and Brimob (Mobile Brigade) personnel. The attack was a particularly brutal one which also took the lives of priests who had tried to negotiate with the attacking forces. There is strong evidence that the attack was actually directed by two TNI officers – Infantry Colonel Herman Sediono (who was also Bupati) and TNI Lieutenant Sugito, who later directed the disposal of the bodies in mass graves. Following this attack several women survivors were reportedly taken to Covalima Kodim Headquarters and sexually assaulted.


34. The massacre at Maliana police-station was the most serious incident in this area, but it was merely the culmination of a wave of violence which began in February 1999. In that month Militia groups launched attacks in Maliana, Atabai, and Cailaco. The Bobonaro/Maliana area militia groups [22]were numerous, and were under the command of Joao Tavares, the militia Panglima, and their operations were inextricably linked with TNI operations, under the command of Lieutenant-Colonel Burhanuddin Siagian. On 12 April six Timorese were kidnapped and then murdered by Halilintar troops. This was followed by a Falintil revenge attack, in which a Halilintar leader and two TNI soldiers were killed. On 13 April a force led by Siagian and Tavares allegedly kidnapped, tortured and then executed six Timorese from Cailaco village, reportedly randomly selected, in revenge for the Falintil killing. From mid-August onwards the militia increased their activities. During this period several murders were committed and houses burnt. On the last day of the election campaign militia attacked Memo, killing 3 persons and destroying 20 houses. On 2 September two UNAMET local staff were shot dead by a TNI sergeant. At the same time, Lieutenant Colonel Burhanuddin Siagian is reported as having told UNAMET local staff that they would be killed after the Consultation.[23] The Halilintar and Dadurus Merah Putih militias, backed by the TNI began a campaign of destruction in Maliana on 4 September, during which several local citizens were killed.

35. The main massacre occurred at the Maliana Police Station on 8 September when Dadurus Militia Putih Militia, backed by TNI troops, attacked a large group of Timorese who were seeking refuge in the police station. According to Interfet investigators, more than 70 persons were killed, many of them in a brutal matter. According to one of these investigators, the TNI were positioned around militia killers, who had reportedly be given drugs, and shot Timorese attempting to escape from the scene.[24] A characteristic of all these operations was the involvement of the TNI at all levels.


36. The eastern districts of East Timor did not suffer the same level of violence, and several villages, among them Uatolari and Viqueque, virtually escaping destruction by the militia. Individual acts of violence or killing did begin early, however. On 17 March 1999 Mariano Soares, a prominent citizen of Triloka village disappeared, and is believed to have been killed. A week later another Timorese was killed by TNI troops in the Baucau district. On 17 April members of Team Alpha killed Virgilio de Sousa, a prominent independence supporter in his home in Bauro Village in Los Palos. In August, in the eve of the plebiscite Los Palos village chief, Verissimo Quintas was brutally killed by local militia, following an attack on his house.

37. The worst period for the Los Palos / Baucau occurred well after the plebiscite. On 12 September four Timorese were killed, reportedly by TNI troops, at the Lospalos Military sub-district command, and on the same day 5 persons were said to have been killed at Baucau by Battalion 745 troops. The worst massacre in the area occurred on 25 September, five days after INTERFET troops landed at Dili. Team Alfa members killed and mutilated nine people, including nuns and deacons and an Indonesian journalist, on the road between Los Palos and Baucau. The bodies were placed in their vehicle which was then pushed into the Luro River. Team Alpha operated under the control of Kopassus officers, and the local TNI commander. According to the KPP HAM report a member of Kopassus was implicated in the ordering of this killing.


38. The Maubara-Maubara district was one of the first areas to experience militia violence. As early as 30 January, Mahidi militia were reported to have killed a civilian in the Liquiça district. It was also in Maubara that the Church came under an early threat. BMP militia members surrounded the Carmelite Convent there on 16 March, and threatened to kill any who tried to leave. On 5 April the same militia group, assisted by TNI troops and Mobile Brigade personnel assaulted a pro-independence group in Maubara, killing two of them. They then went to Liquiça, where they proceeded to burn the houses of known pro-independence supporters. They then surrounded the Liquiça Church, where more than 1,000 people were assembled. After some attempt at negotiation, the compound was attacked, and more than 50 killed, [25]with the bodies being disposed of with TNI help. Occurring as it did while the 5 May Agreement was being negotiated, the incident aroused a strong international reaction. However, General Wiranto told journalists in Jakarta that both pro-integration and pro-independence groups had become “emotional”. Interviews of Liquiça residents, and a study of records held by Civpol and SCIU indicate the TNI and Mobile Brigade personnel played a leading role in the attack, and the disposal of the bodies.

39. Other areas where militia killings took place were the Manatuto, Aileu, Ermera, Ainaro and Manufahi districts.

XI. Responsibility for the Crimes Against Humanity

40. The campaign of violence and terror which was conducted in East Timor from April to October 1999, is usually described as “militia violence”. While militia members played a key role in these operations, the term needs some qualification. There is strong evidence that questions the widespread assumption that the first line of responsibility rests with the militia leaders. A number of these leaders clearly bear a responsibility for leading, or participating in, attacks on groups and individuals, for the intimidation of local populations, and for their participation in the mass deportation of peoples in September, and the wholesale destruction and ransacking that accompanied it. A number of militia members have already been arrested and are awaiting trial in Dili. However, as has already been pointed out, most of the offending leaders, such as Eurico Guterres, Manuel de Sousa and Joao Tavares, are now in Indonesia, and the further pursuit of investigations against them is critically dependent on cooperation from the Government of Indonesia. Despite encouraging responses from President Wahid and Attorney-General Marzuki Darusman, the attainment of an appropriate level of cooperation is not yet assured.

41. The militia leaders, therefore, may be the most conspicuous subjects for prosecution, but they are not really the most important subjects for investigation in relation to these serious human rights violations. In his report on UNAMET, its chief executive, Ian Martin, later wrote:

Observers had little doubt that the Indonesian armed forces (the TNI) were responsible for forming and arming the pro-integration militia groups, and for directing their activities. While this was officially denied to international critics there was no concealment of the degree of official approval of their existence: military, police and civilian officials attended inaugural and other functions throughout the territory. The culmination was a parade ceremony in front of the Governor’s office in Dili on 17 April, in the presence of senior officials, at which Joao Tavares of Halintar and Eurico Guterres of Aitarak spoke as Commander and Deputy Commander respectively of the militias’ umbrella organization.

42. Their operations were the intended result of operations planned, in the first instance, by certain senior officers of the Indonesian National Army, the TNI, with the collusion, at least, of the civil government. It also needs to be taken into account that the Indonesian province was dominated by the military. There were more than 17,000 troops in the province, and TNI officers had a commanding presence in key areas of government, and in the districts. Here it is also worth noting that at the time of their departure in 1975 the Portuguese garrison amounted to a mere 200 soldiers, most of them non-combatants. The commanders also had extensive property interests. Timor also received close attention from Kopassus, the special forces command, which had played a lead role in the TNI’s covert intervention in 1975. Its structure and role will be considered else where in this report. Who then were the commanders behind the scenes? These include senior officers of ABRI Headquarters, the officers in command of the East Timor Korem 164 command, and the Nusatenggara regional, or Kodam/Udayana command, of which the East Timor territorial command forms a constituent part, and several commanders at the district level, in particular the Dili area, and the kabupatens of Liquiça, Bobonaro, and Covalima. In the first instance the militia were trained by, and equipped by the TNI, and there is evidence based on the investigation of militia members that orders were given to attack and kill their targets who were invariably unarmed. There are, I believe, sufficient grounds to consider the prosecution, in particular, of Major General Syafrei Syamsuddin, Major General Zakky Anwar Makarim, Major General Damiri, Udayana commander, Brigadier General Tono Suratman and Lieutenant Colonel Yayat Sudradjat. These officers were the leading actors in what was in effect a conspiracy to implement a campaign of violence against the unarmed supporters of the independence option; the deportation of a large part of East Timor’s population; and the wanton, indiscriminate destruction of their houses, and other buildings essential to the well being of village and town communities. These names are a select list only. In terms of responsibility, to this list should be added the names of other officers, militia unit commanders and members, both of the militia and the TNI. In most cases the militia may have been identified as the killers and agents of the reign of terror, but their actions flowed from the command involvement of TNI officers, sometimes from direct orders, or from the provision of military training, weapons, money and, according to militia members, drugs.

43. To elaborate on this last point it needs to be stressed that the emergence of the militia in East Timor was not a spontaneous public response, reflecting the legitimate concerns of those Timorese who favoured remaining with Indonesia. The formation of this para-military organisation was planned by a group of TNI officers as a cover for their own strategic objective of preventing the loss of the Province to the Republic of Indonesia. In practice it meant preventing the fulfillment of the efforts by the United Nations and members of the international community to secure for East Timor a genuine act of self-determination, which had long been urged by the United Nations General Assembly, and was explicit in the May 1999 Agreement concluded in New York between Indonesia, Portugal and the United Nations. While a minority of East Timorese evidently preferred the autonomy proposal over a shift to independence, probably only a small proportion of this number favoured resorting to violence in support of their cause. Even those who became members of the militia may not have resorted to the use of violence to advance their cause, had they not been incited, encouraged, trained and equipped to do so by officers of the TNI. As militia operations intensified in 1999, many Timorese, some of them under age, were conscripted as recruits, while those who tried to withdraw from the organization were sometimes hunted down and punished.

44. An example of the comprehensive TNI control over militia operations has been described in an article by Peter Bartu, who served as a political officer in the Maliana, one of the strongest militia areas, and one of clear strategic importance because of its proximity to West Timor. Bartu’s excellent report[26] highlights the extent of TNI control over the militia groups in that particular district, as well as the involvement of the civil administration. He concludes:

“The TNI were heavily involved in all aspects of militia activity in Bobonaro district aimed an ensuring a pro-autonomy vote in the Popular Consultation. At the higher levels the sub-district militia leaders were coordinated and directed by the Dandim and his intelligence chief from the Kodim and from the Bupati’s office. At the sub-district level the militia was either directly commanded by TNI personnel or directly supported by Koramil staff. At the village level the militia worked hand in hand with military posts and Babinsas.”[27]

45. These conclusions are in general terms consistent with the findings set out in the report by Indonesia’s KPP HAM, which has been brought to my attention. Its conclusions are similar to those I have reached in the process of this investigation. For example, in Paragraph 3 of its press release the KPP HAM report states as follows:

“KPP HAM has succeeded in assembling facts and evidence which indicate strongly that serious violations of human rights were carried out in a planned manner, systematically on a large and widespread scale, in the form of mass murder, torture and oppression, forced disappearances, violence against women and children (including rape and enslavement), deportation, scorched earth destruction and damage to property, all of which constitute crimes against humanity.”[28]

46. It concluded, moreover, that:

“These facts and evidence also indicate that the civil and military establishment, including the police, acted in cooperation with the militia, in creating situations and conditions which supported the carrying out of crimes against humanity, which were carried out by civil, military, police and militia agencies.”[29]

X.      The Commanders

Indonesian Military Officers Involved in Crimes Against Humanity

47. Annex A to this report contains a list of officers whose roles would have placed them in positions of responsibility in relation to the crimes against humanity that occurred in East Timor in 1999. In some cases their responsibility may have been peripheral. Others have a much greater complicity. At the top of the list must stand the generals who planned the formation of the militia, providing its units with arms, money, targets, and with drugs to be taken by members to ‘make them brave’ when on operations. These include Major General Zakky Anwar Makarim, Major General Syafrei Syamsuddin and the regional operational commanders, Major General Adam Damiri, Colonel (now Brigadier General) Tono Suratman and Lieutenant Colonel Yayat Sudrajat, who passed on orders and advice to militia commanders. Others, the KPP HAM report found, failed to meet their responsibilities according to Indonesian law. All TNI commanders of districts in which major violations occurred cannot escape a measure of responsibility, especially where TNI troops led or assisted the militia. No military commander can shirk responsibility for the behaviour of men under his command, whatever the circumstances, particularly when they bearing arms that were issued to them. Most of the troops of Battalions 744 and 745 were of course East Timorese, and many of them became active in the militia groups. In judging their activities, however, they should be considered first as members of the TNI, especially when they wore uniforms and carried weapons. The responsibility of soldier’s conduct, when he is combat dress, must remain ultimately with the officers in command of his unit. Therefore, if a Timorese soldier in combat dress joined in militia operations he should, I suggest, be considered a member of the Indonesian National Army.

48. It would be an injustice to condemn all TNI officers in the Udayana/East Timor command for the crimes against the people of East Timor in the period covered by this report. We know that at least some were troubled by the TNI’s involvement in the militia violence. On the other hand, most of those in command positions in the areas in which these crimes occurred must have known that serious abuses were being perpetrated, and that there was a measure of TNI involvement. The massacres that took place in Dili and Liquiça in April 1999 – not to speak of the many incidents of individual killings, almost all of them by militia units, offered ample warning to military commanders that the militia they had created were unconcerned about basic human rights. While there were reassuring statements by senior officers in Dili there is little evidence of any serious effort to implement their assurances. The reality behind the scenes suggests that at least some military commanders were exhorting the militia to kill. According to Tomas Gonçalves Colonel Tono Suratman himself explicitly stated that all CNRT (members), priests, nuns and pro-independence leaders should be regarded targets for ‘elimination’. A similar statement was reportedly made by Governor Abilio Soares on 26 March. According to other testimonies, in August at least some senior commanders exhorted the militia to kill, and to use violence against officials of the Church. Indeed, in the case of the Suai massacre Colonel Sediono was reported to have been giving orders to the militia, who at that time were killing people in the Ave Maria church, including priests. Sediono, who was Bupati of Cova lima at that time, may have been occupying a civil administration post, but the fact that for his role in the massacre he reportedly donned a TNI uniform and brandished a weapon indicates the he was performing a military function. Some officers, usually at a lower level – such as Lieutenant Sugito of Covalima and Lieutenant Sayful of Lospalos - participated actively in leadership roles in militia operations. In most militia operations it may well have been that TNI commanders were not present, but as their troops were involved they could not have been unaware of what was going on Thus we have three categories of commanders: those involved directly in the militia operations in a command sense (nearly all of them Kopassus officers): those who were indirectly involved: and those who kept a discreet distance from all aspects of these operations, but who would almost certainly have been involved the mass deportations of September 1999.

49. The extent to which Indonesia’s Armed Forces High Command was involved in this operation is still not clear, but it is difficult to believe that General Wiranto, for example, could have been unaware of Operasi Guntur, not least because of the magnitude of an operation which succeeded in transporting some 250,000 East Timorese to Indonesian Timor over a period of less than a fortnight, and in destroying or seriously damaging more than 70% of homes and buildings in East Timor. This operation required considerable organizational skill and the mobilization of transport and other military resources. It seems inconceivable that these resources could have been mustered without the prior knowledge and approval of the head of Indonesia’s armed forces.

50. In this connection the authors of the KPP HAM report noted that they:

‘had been able to ascertain from the entire process of investigation, including the gathering of facts and documents with the testimony of witnesses and other parties (pihak-pihak lainnya)[that] all of the human rights violations, which were widespread and organised, which occurred both before and after the plebiscite in East Timor, were well known to and understood by the ABRI Panglima/TNI General Wiranto as the person responsible for national security, along with all levels of civil and military officials, in the context of their responsibilities and operations in East Timor at that time.’[30]

51. The Report goes on:

‘The entire crimes against humanity in East Timor occurred, directly or indirectly, because of the failure of the TNI Panglima to guarantee the security of those carrying out of the two options announced by the Government. The police structure, at that time under the Ministry of Defence, weakened the capacity of the police to implement the security precautions based on the New York agreement. For this, TNI General Wiranto, as TNI Panglima, is a party who must be held responsible.’[31]

52. In his monograph, Professor Des Ball wrote that, in connection with the TNI plan for ‘violent retribution’, Australian intelligence agencies had

“identified the senior Indonesian military officers involved, and reported that the chain (of command) reached up to General Wiranto, the Commander in Chief of the TNI, and that implementation of the plan was the responsibility of the TNI’s SGI (Satuan Tugas Intelijen, or Combined Intelligence Task Force), directed by Kopassus..”[32]

53. In this paper I have unashamedly focused on the TNI commanders, without whose intervention the militia violence would never taken place, except perhaps on a quite minor scale. The TNI commanders not only nurtured the militia into existence; they also stiffened the resolve of individual groups, and in at least some cases encouraged their brutality. This is not intended, however, to play down the individual guilt of the militia leaders. No doubt as committed supporters of integration they willingly, if not enthusiastically, accepted their leadership roles. On the other hand, their involvement is easier to identify, and the prosecution case easier assembled, although in some cases, such as those of Joao Tavares and Eurico Guterres, the Militia offenders are, at this juncture, as inaccessible as are the TNI commanders. Then there are civil administration officials, whose involvement is well known. The KPP HAM report lists Abilio Soares, the Governor of East Timor, Domingos Soares, the Bupati of Dili, as well as the bupatis of Covalima, Liquiça, Bobonaro, Lospalos as among those implicated in the crimes against humanity.[33] Many civil officials at lower levels, of similar political disposition, became members of the militia, in some cases after considerable pressure from their superiors, militia leaders, or the TNI. While most of these officials were not themselves involved in the killing or other crimes, at least some, such as Abilio Soares, used their considerable authority to encourage activities which resulted in crimes. In the circumstances they must at least be considered accomplices.

54. In Annex A I have assembled a list of TNI officers, based on information collected in East Timor and on data assembled by Dr. David Bourchier, an academic specialist on the Indonesia military at the University of Western Australia.[34] While there is a prima facie case, I believe, for some of those on this list to be charged with crimes against humanity, other names are included because of the command positions they held in areas where serious incidents occurred. The list includes some background details, which are designed to help with the identification of the persons concerned. A number of officers on this list were also listed in the KPP HAM report. This information may serve as useful reference for investigators and prosecutors.

XI.          Sources of Information and Acknowledgements

55. The information contained in this report is based on an examination of documents held by agencies of UNTAET in East Timor, including the records made available by the Serious Crimes Investigation Unit, Civpol, military assessments, UN reports and assessments, interviews of UN officials, Interfet officers and, not least, East Timorese, the KPP HAM report, a Yayasan Hak report, a report by FOKUPERS, NGO reports and accounts in the media. I have also made use of some thousands of email items on the unfolding drama in Timor accumulated during 1998/99. My conclusions are based on a considered evaluation of these sources, against the background of my own lengthy experience as an analyst and chronicler of events in both East Timor and Indonesia. The conclusions and views expressed herein are of course essentially my own

* * * * * * *

[1] See Situation of human rights in East Timor – Note by the Secretary General, 8 December 1999

[2] See KPP HAM report, 16 August 2000.

[3] ICI Report, para 150.

[4] See P.21 Report by the Special Rapporteur, Mr. Bacre Waly Ndiaye, on his mission to Indonesia and East Timor from 3 to 13 July 1994 (in E/CN.4/1995/61/Add.1)

[5] Harold Crouch: Indonesia: Impunity versus Accountability for Gross Human Rights Violations (ICG Asia Report No. 12, Jakarta/ Brussels, 2001)

[6] Harold Crouch: Op cit. P. 30.


[8] See KPP HAM report, para 27, Press release.


[10] See Ian Martin,

[11] This operation was referred to in a leaked militia document, dated 11 March. In it the Militia commander, Lafaek Saburai, informed Joao Tavares that his group would carry out Operasi Sapu Jagad to ‘exterminate the leaders, cadres, and supporters of the anti-integration movement. This brutal plan was not carried out, but in April there was a surge of killings in some sectors.

[12] See Tomas Goncalves: Transcription of testimony.

[13] Battalion 744 came under the command of Major Yunus Yosfiah, who had led the attacking force into Balibo

[14] See Dunn, James: Report on Talks with Timorese Refugees in Portugal (Canberra, Parliamentary Library, 1977)

[15] See “Indonesia Confronts Unruly Past”, article by Dan Murphy, in Christian Science Monitor, 20 Nov. 2000.

[16] See Silent Witness, p 36, a report prepared by Professor Desmond Ball,
Director of the Strategic and Defence Studies Centre, Australian National University, Canberra, 2000.

[17] See Peter Bartu: Op cit

[18] See Peter Bartu Op cit. P 2.

[19] Serka – Top Sergeant.

[20] For more details on the militia structure and its operations, see “Laporan Pelanggaran Hak Asasi Manusia, Januari – September 1999, Chapters IV and V ( Yayasan Hukum, Hak Asasi dan Keadilan Timor Timur)

[21] See FOKUPERS: Progress Report: Gender-based Human Rights Abuses during the Pre and Post-Ballot Violence in East Timor, January – October 1999 (Dili, July 2000).

[22] Although Halilintar was the leading group, there were at least six other militia groups, including the notorious Dadurus Merah Putih, led by Natalino Monteiro.

[23] Peter Bartu – Op cit. p.11.

[24] Based on an interview of an Australian intelligence officer, who was among the first troops to reach Maliana.

[25] According to my talks with Liquica residents, the total killing around that event in fact amounted to more than 200!

[26] Peter Bartu – The Militia, the Military and the People of Bobonaro District (unpublished paper)

[27] Peter Bartu - Op.cit. P.11.

[28] Laporan Lengkap KPP HAM, 16 August 2000.

[29] KPP HAM Report – Para 6, Press release.

[30] KPP HAM Report, Para 192.

[31] KPP HAM Report, Para 192.

[31] HAM Report Para 193.

[32] Prof. Des Ball – Op cit p.19

[33] KPP HAM Report: Para graph 191.

[34] David Bourchier – Key People in the Chain of Command Responsible for East Timor (Department of Asian Studies, University of Western Australia)

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