Craig Skehan – An official history of Australia's role in East Timor's transition to independence reveals that the Federal Government knew more than it was willing to admit at the time about orchestrated Indonesian military violence.

However, the official account maintains that Australia had not been in possession of hard evidence that the conspiracy was directed by the military's top brass in Jakarta.

Foreign Minister Alexander Downer said yesterday that "outrageous" allegations had been made about Australia's role in the self-determination process. This had included claims that Australia failed to disclose Indonesian military plans for post-referendum massacres because of fears it would offend the Indonesian Government. Mr Downer said the aim of East Timor in Transition 1998-2000, an Australian Policy Challenge, was to set the record straight.

However, the Opposition's foreign affairs spokesman, Laurie Brereton, said taxpayers' funds had been spent on a "highly selective and partisan account" intended to repair damage to Mr Downer's credibility. He said Mr Downer could not escape from the fact that Australia argued against pressing Jakarta to accept an international peacekeeping force for the August 30, 1999, vote.

The new account confirms that, in the weeks leading up to the ballot, Australia did not believe that a peacekeeping force was achievable. However, it states that the Prime Minister, Mr Howard, during an April meeting in Bali, personally pressed Indonesia's President Habibie to accept a peacekeeping force.

Indonesia had strongly rejected the proposal and the Australian Government concluded that pursuing it further would have risked Indonesia cancelling the whole self-determination process.

The Australian Government's account, written by Foreign Affairs Department officials, stressed that Australia had suggested to Indonesia a period of at least several years' autonomy before a vote on independence. President Habibie nonetheless opted for a quick ballot.

The military's "credibility" had earlier been eroded with its announcement in December 1998 that it would arm civilian volunteers. "Over the first months of 1999, a pattern emerged of militia violence and intimidation against independence supporters with extensive TNI collusion," the book, based on both public sources and diplomatic cables, states.

"This phenomenon was to generate intense international alarm – not only over the plight of East Timorese who fell victim to the terror campaign, but over how to ensure that these new militia groups, abetted by the military, did not derail the historic opportunity for a lasting resolution to the East Timor issue."

The book said TNI's real attitude towards East Timor in the period leading up to the ballot was "difficult to gauge" because of mixed messages and conflicting information.

"Progressively, throughout the first months of 1999, however, TNI's actions in East Timor revealed a commitment to retention of East Timor as part of the Republic," the book says.

"By March, Australia started seeing the evidence of a dual policy at work: a declaratory policy of neutrality consistent with Habibie's commitment to a free ballot, and a covert policy that sought to ensure an outcome in favour of autonomy.

"There was a belief that intimidation could be an effective means by which to influence the way in which the East Timorese would vote and, by the middle of the year, it was evident that TNI was encouraging and supporting militia groups in pursuit of this goal."

At the time, Mr Downer referred publicly to what he dubbed "rogue elements" of the Indonesian military being actively involved in militia violence. But the new account states: "The reality was that the militia were established with the support and encouragement of TNI, with the clear objective of undermining the independence cause."

Of the militia groups, it is said; "Many were attracted to the violence, others were press-ganged, still others did it for money or other inducements, including drugs and alcohol."

Underscoring Australia's official knowledge of strong links between the military and militias, the book says it was clear that militia excesses were conducted with "impunity and the acquiescence" of the Indonesian military although it was "not possible to determine the extent to which TNI's actions on the ground were sanctioned by, or ordered, from Jakarta".

But Mr Downer said at a press conference yesterday that statements being made at the time by military head General Wiranto on attempts to stem militia attacks at the very least had the hallmarks of a "PR exercise".