Karen Michelmore and Olivia Rondonuwu, Bali – Indonesia could not have anticipated the scale of violence that followed East Timor's historic 1999 vote for independence, Indonesia's former foreign minister insisted today.

Ali Alatas has told a landmark public hearing that he feared discord among rival factions if East Timorese were given a choice between full independence and the alternative offer of being an autonomous province within Indonesia.

Alatas said he feared those who lost out in the UN-sponsored referendum would not accept the result.

He was right but today said the scale of the unrest that followed the pro-independence vote came as a "painful surprise" to both Indonesia and the United Nations.

Alatas faced questioning over Indonesia's role in the destruction in East Timor at today's landmark opening of a public hearing of the East Timor-Indonesia Commission of Truth and Friendship.

The commission, sitting on the Indonesian resort island of Bali, is seeking to establish the truth behind the 1999 violence which killed up to 1,500 people in East Timor before and after the UN-sponsored ballot.

Alatas spoke today of a December 1998 fax from Australian Prime Minister John Howard, suggesting Indonesia grant temporary autonomy to East Timor for 10 years. But he said the suggestion angered then Indonesian President BJ Habibie and triggered Jakarta's decision to give the Timorese a vote for independence.

Howard's "carefully written" fax said Australia supported Indonesia and its offer of wider autonomy for East Timor but Australia's research suggested it would not work, Alatas said.

"So on January 25, after the letter arrived formally... the president made the decision, the decision we all know," he told the hearing.

"He was a bit angry and wrote his disposition on that letter. He said 'what's the use waiting five, 10, 15 years, we will always be criticised if anything happens but we will still have to spend a lot of money and after 10 years they will say goodbye to us'.

"So if they want independence now, give it to them, a second option for them to choose."

Alatas said he felt "uncomfortable" about the decision to give the Timorese a choice between wider autonomy and independence as he felt those who lost would refuse to swallow the result.

"My worst fears were confirmed as soon as the announcement was made, those who lost did not accept it," he said. "But I could not anticipate that it would take this form, this incredible form."

Alatas said he was not aware of any Indonesian government decision or policy that directly caused the unrest in East Timor. He expressed frustration about the criticism Indonesia continues to face over East Timor.

"Indeed it is a fact, especially after the (Santa Cruz Massacre) 12th November 1991, there is lots of criticism of Indonesia, nothing that Indonesia can or will do is right," he said. "They are indeed prejudiced, anti-Indonesian".

The Santa Cruz Massacre, also known as the Dili Massacre, was one of the most notorious events in a resistance war several East Timorese groups fought against Indonesian forces for independence.

More than 250 East Timorese were killed by Indonesian troops in the Santa Cruz Cemetery in Dili, the images secretly caught on video and broadcast around the world.

Alatas said that after the independence vote, Indonesia continued to consider itself responsible for security in the province and did not want foreign troops on Indonesian soil.

It was not until military chief General Wiranto saw the scale of the violence following the ballot that he changed his mind, and the Australian-led UN mission entered East Timor restore peace, Alatas said.

"I think he had no idea until he entered Dili, he had no idea what was going on there in my opinion," he said.

"When he arrived, he saw the destruction that had taken place, how many houses had been burned... then he saw that he couldn't handle the situation as it was alone. So at that time... he asked the UN to come and assist."

Alatas said Indonesia and East Timor needed to continue to work together to settle their differences.

"Let us look forward and not continuously look backward," he told the hearing.

"I think this is what we countries must try to do, it's in the interests of both that we are are closer.

"For Indonesia, a Timor Leste in turmoil... divided and not progressing, that's a danger for Indonesia because after all, they are part of the archipelago and if something is wrong it will have an impact on us."

The hearing continues this afternoon, with testimony from one of the victims of another attack at Liquica Church, blamed on pro-Indonesia militias and soldiers in which more than 200 people died.

The commission plans to hold five public hearings from February until June, and hear from 78people including Wiranto, former president Habibie, former militia leader Eurico Guterres and East Timor president Xanana Gusmao.

Gutteres is the only person serving a prison sentence for his role in the 1999 violence.