The only Indonesian jailed over the violence surrounding East Timor's historic 1999 independence vote has apologised to Indonesia for the unrest that tainted its international image.

Pro-autonomy militia commander Eurico Gutteres also called on the people of East Timor to unite and move past the violence of the past, in order to build a strong independent nation.

He said he hoped to one day travel to the tiny nation to personally apologise to victims' families, adding he was ready to face justice in East Timor.

"Let us leave the past behind, let's look to the future," Gutteres told an East Timor-Indonesia commission into the 1999 violence.

"Leave behind all the egos, all the hatred we have accumulated over 24 years. I hope there will be no more deaths, no more victims, no more tears in this independence... build on this independence so it can be a strong independence."

The East Timor-Indonesia Commission of Truth and Friendship (CTF) is holding a series of public hearings as it seeks to establish the truth behind the violence before and after the 1999 poll, in order to aid reconciliation between the two nations.

Some 1,500 people were killed and hundreds of thousands displaced when pro-Indonesia militia linked to the Indonesian army went on a killing and arson spree across the tiny nation.

In 2002 Gutteres, the former head of the Aitarak militia, was sentenced by a special Jakarta human rights court to 10 years' jail for his role. He began serving his sentence in May last year.

He was accused of causing dozens of deaths by allowing his militia gang to go on a rampage after the overwhelming vote in favour of independence.

Gutteres on Wednesday said he did not kill anyone, but accepted responsibility for the deaths.

"I didn't kill people," he told the packed hotel conference room. (But) what I have been accused of, and found guilty of... in my capacity as the vice commander, I am responsible for the actions of my men."

Outside the hearing, he told reporters he did not expect to receive amnesty for his testimony.

In an at times rambling but passionate address to the commission, Gutteres described the violence that shook East Timor eight years ago as a "tragedy of humanity", and said people on both sides – pro-independence and pro-Indonesia – were killed and committed violence.

With distinctive long curly hair, and dressed in a black suit and bright red tie, Gutteres also read an "open letter to the nation of Indonesia" apologising for tarnishing its image in the international community.

"On behalf of the pro-integration (East Timorese) and their families, we extend our apologies from the deepest depths of our heart to the Indonesian nation," he said.

But he said Indonesia was not without blame for the carnage, saying the governments of Indonesia and Portugal, as well as the United Nations, were at fault for handing East Timor the divisive vote without first ensuring the environment was secure.

Gutteres said all three should apologise to East Timor "for the neglect of the situation and their irresponsibility".

He was also scathing in his criticism of the CTF as a body to seek the truth, saying it should be expanded to investigate the litany of violent episodes in East Timor outside 1999. "If the CTF... only limits itself, the truth, reconciliation and friendship – we will never find it."