Reporter: Geoff Thompson
Mark Colvin: Indonesia's former Foreign Minister, Ali Alatas, has identified a letter from John Howard as the factor that pushed former President Habibie to support a referendum on East Timor's independence.
Mr Alatas was speaking at the opening session of a new Truth and Friendship Commission set up to establish the facts of the violence surrounding the independence vote in 1999.
Modelled on South Africa's Truth and Reconciliation Commission, the joint Indonesian and East Timorese body has no power to recommend prosecutions.
But it can recommend amnesties for human rights abusers who cooperate with it. Our Indonesia Correspondent, Geoff Thompson, is at the hearing and he filed this report from Bali.
(Sound of gunfire)
Geoff Thompson: It is the violent events of 1999, seven-and-a-half years ago which are the focus of the long gestating Truth and Friendship Commission, which began hearing testimony in Bali today.
In theory at least, the Commission is modelled along the lines of South Africa's Truth and Reconciliation Commission. And like that body, this joint Indonesian and East Timorese effort can recommend amnesties for witnesses who are forthcoming and cooperative.
A United Nations-supported report by the Commission for Reception, Truth and Reconciliation released this time last year, was vast and damning of Indonesia.
It blamed Indonesia's security forces for the deaths of 183,000 civilians, mostly through hunger and illness, as well as most of the 18,600 killings and disappearances between 1975 and 1999.
Those findings were largely buried by Indonesia's President Yudhoyono, and his East Timorese counterpart, Xanana Gusmao.
But today's bipartisan Truth and Friendship Commission has their full support. As a way of addressing the past, and getting on with the future.
The first to appear was Indonesia's Foreign Minister in 1999, Ali Alatas. He detailed how he pushed for special autonomy for Indonesia and said that it was a letter from John Howard to the then President BJ Habibie, which set East Timor on its troubled path to independence.
Mr Alatas said the Australian Prime Minister's suggestion of an interim autonomy period angered Mr Habibie, who saw it as a waste of time and money, and likely to attract further international criticism of Indonesia. Instead, Mr Habibie decided to let East Timor decide its future for itself. After his testimony, Ali Alatas sounded more diplomatic.
Ali Alatas: It was a letter which indeed pushed things as far as President Habibie's views were. But it was quite a good, quite a normal letter.
Geoff Thompson: Do you think the transition or the change or the options might have run smoother if that letter didn't arrive?
Ali Alatas: No, it's not the letter you know which is the bone of contention between the two. It was rather the spirit of overzealousness of Australia suddenly to send troops and send the largest contingent of troops. Sometimes it's a gung-ho attitude etcetera. It was not the letter, it was not the letter.
Geoff Thompson: Ali Alatas also suggested there was bias and even perhaps even electoral dishonesty on the side of the United Nations in favour of independence, and said he could not explain why the vote for independence was so overwhelming when he believed most people in East Timor supported integration with Indonesia.
He also maintains that the police and not the military were responsible for securing the ballot in 1999, and says he had no evidence that the military were really pulling the strings.
Ali Alatas: The Foreign Minister does not know everything the military does. Does your Foreign Minister know?
Geoff Thompson: So, you didn't know that the military was unofficially and directly involved?
Ali Alatas: I don't have any evidence about what you're saying.
Geoff Thompson: But you know it's generally accepted that the military were behind the militia.
Ali Alatas: I don't have any evidence about what you're saying.
Geoff Thompson: But that doesn't mean it didn't happen.
Ali Alatas: I don't know.
Geoff Thompson: There were few East Timorese at the hearing today apart from the six commissioners taking part. Some of them were human rights activists back in 1999, and looking anxious and disconcerted by the proceedings, they declined requests for interviews.
The East Timorese co-chairperson, Dionisio Babo Soares, said he was aware that the Commission was open to criticism that it is rewriting history and emboldening a culture of impunity in Indonesia, which has seen so few human rights abusers brought to justice.
Dionsio Babo Soares: We will try very hard from our side at least to strengthen the relationship, but we also have to recognise, and I hope this should be recognised by everyone in East Timor and in Indonesia including the commissioners from Indonesia that truth must be revealed and must be established. Without truth, there will not be any long lasting friendship.
Geoff Thompson: Future sessions of the Commission are expecting to hear from Indonesia's former military chief, General Wiranto and the jailed militia leader, Enrico Gutierrez.
In Bali, this is Geoff Thompson for PM.