The federal government has sidestepped accusations it wanted East Timor to remain a province of Indonesia and delay its bid for independence.
The final report of East Timor's truth and reconciliation commission says Foreign Minister Alexander Downer wanted to delay the 1999 poll by several years.
The commission, known by its Portuguese acronym CAVR, has been collecting evidence from thousands of witnesses for the past three years about Indonesia's annexing of the former Portuguese colony in 1975.
Its 2,500-page report, which shows that up to 183,000 East Timorese died as a result of the 24-year occupation, was handed to the United Nations two weeks ago.
The commission found that Australia "contributed significantly to denying the people of Timor-Leste their right to self-determination before and during the Indonesian occupation".
It also says it was in Australia's interests for East Timor to remain part of Indonesia. Mr Downer wanted to delay the vote, CAVR says.
"The commission finds that, even when (former president BJ) Habibie was moving towards his decision to offer the East Timorese a choice between remaining part of Indonesia and independence, the Australian Foreign Minister Alexander Downer made it clear that his government believed that it should be several years before the East Timorese exercised their right to make that choice and that it would be preferable from an Australian point of view if Timor-Leste remained legally part of Indonesia."
But the Department of Foreign Affairs and Trade (DFAT) has now said Australia made it clear at the time it supported self-determination for East Timor.
"Australia's policy position at the time was clearly articulated that reconciliation in East Timor be would best served by the holding of an act of self-determination and the issue was essentially a matter for the parties involved to resolve," a DFAT spokesman said.
"Australia consistently urged that the East Timorese be directly involved in the consideration of their future and made it clear that Australia would accept an outcome negotiated between East Timor and Jakarta." The East Timor government had not yet officially released the CAVR report, the spokesman said.
Australia accepted the result of the result of the referendum held in 1999, in which the East Timorese voted overwhelmingly to break free from Indonesia.
But the Commission for Reception, Truth and Reconciliation said Australia violated its obligations under international law by backing the bigger neighbour's push to take over East Timor in 1975.
Australia was influenced by a desire to get the most it could out of maritime boundary negotiations affecting oil and gas reserves in the Timor Sea, it found.
"The commission finds that during the Indonesian occupation successive Australian governments not only failed to respect the right of the East Timorese people to self-determination, but actively contributed to the violation of that right."
Labor says it will be raising the matter in parliament when it resumes next week.