Blair "undermined U.S. policy in the run-up to the referendum in East Timor," said Edmund McWilliams, who was political counselor at the U.S. Embassy in Jakarta at the time.

"While we (U.S. diplomats) were pressuring the (Indonesian) military to rein in its militias and stop their intimidation of voters, Blair went out of his way to befriend senior officers, especially (Defense Minister) Gen. Wiranto," McWilliams told United Press International.

Wiranto, who like many Indonesians uses just one name, was indicted in 2003 by a U.N.-backed court in East Timor for his role in the 1999 violence, which cost hundreds of lives before the referendum, and thousands after it.

As Pacific Command chief, Blair's "virtual silence on the (Timor) issue in meetings with the Indonesian generals led them and their militias to escalate their attacks on the Timorese," said McWilliams.

"This is a relevant issue today, because partnering with bad militaries is something we have done a lot of (as part of the war on terrorism) and something we should be concerned about," he concluded.

Blair could not be reached for comment, and nominees traditionally do not speak publicly ahead of their confirmation hearings. An administration official told UPI that U.S. policy was to work "to bring about East Timorese independence and to stop the abuses by the Indonesian military."

The official said Blair's actions were "in accordance with U.S. government policy at the time," adding, "Blair condemned the conduct of Indonesian troops in East Timor, and he conveyed that if they behaved responsibly, the United States was prepared to resume normal relations. If they did not, they risked further negative consequences."

Observers said questions likely also will be raised about his judgment in relation to an alleged conflict of interest during his tenure as head of the funded research center called the Institute for Defense Analyses after he retired as head of Pacific Command in 2002.

Watchdog non-profit the Project on Government Oversight found that Blair had overseen an assessment by the institute of the new F-22 military aircraft while being a stockholder and board member for two subcontractors working on the plane.

A Defense Department inspector general report found he had breached conflict-of-interest standards, and Blair resigned as head of the institute.

But few expect Blair to get a hard time at Thursday's hearing. "I don't think those issues are going to pose much of a challenge," said Christopher Preble, director of foreign policy at the libertarian Cato Institute.

Supporters point to his long experience in intelligence and say he is an "out of the box" thinker. In February 1999, for instance, when he took over as chief of Pacific Command, he established the Virtual Information Center, an open-source intelligence collection and analysis unit. According to a fact sheet provided by Pacific Command public affairs staff, the center is staffed by contractors operating outside the traditional military intelligence and operational structures "to provide a separate, independent view" of regional issues.

The center's products "complement (the) classified intelligence picture; (and) provide key data on dominant Asian press discourse including Asian reactions to domestic and world events," states the fact sheet. Because they are unclassified, they also can be shared instantly with Pacific Command's international partners.

The center's four contractors use non-military Internet accounts "to allow access to Web sites that block .mil accounts and to facilitate communications with non-government entities," the fact sheet says.

But the questions that are likely to concern senators on the Intelligence Committee relate to big challenges Blair will face in his new job, according to a staffer who asked for anonymity.

"There will be bigger questions for the (director of national intelligence) related to whether our intelligence structure is suited to our current needs," said the staffer, adding that the recently overhauled organizational chart for the nation's spy agencies "absolutely" still needed tweaking. As an example, he said, "The way we set (intelligence) requirements needs work."

In addition, he said, there would be questions about "whether there are still too many big acquisition programs that are a legacy of Cold War thinking."

"We don't have a good road map for where our overhead architecture needs to be in the next 15 to 20 years," the staffer continued, using the intelligence term of art for spy satellites, "and that's the time frame you need to be thinking about, because those things take a long time to build and launch."

Several large spy satellite programs have been slammed as overly expensive or less than efficacious by lawmakers in recent years, although most of the criticisms have been raised in secret, closed sessions, with only an occasional eruption into the public domain.

Preble told UPI such secrecy was "one of the top issues that the new administration has to confront. … How much information really has to be kept out of the public's hands?"

"The burden of proof should always be on those making the argument for secrecy," Preble said.

Last year lawmakers attempted to push several pieces of legislation dealing with what experts call over-classification, the seemingly intractable pressure within intelligence agencies to keep too much of their business secret.