Olivia Rondonuwu, Nusa Dua – Indonesia and East Timor expressed regret on Tuesday for violence surrounding Dili's 1999 independence vote after a joint probe blamed state institutions for "gross human rights violations."

The report by the Commission of Truth and Friendship (CTF) went further than many had expected in blaming Indonesian security forces for the mayhem, although Indonesian President Susilo Bambang Yudhoyono stopped short of an apology.

The two governments set up the CTF in 2005 to look into the violence, during which the United Nations estimates about 1,000 East Timorese died, but it has no power to prosecute, prompting criticism that it serves to whitewash atrocities. It has been boycotted by the UN.

"On behalf of Indonesia and the East Timor governments, we convey deep regret to all parties and victims, who directly or indirectly suffered physical and psychological wounds after serious human rights violations that occurred ahead of and soon after a ballot for independence in East Timor in 1999," the countries said in a joint statement.

The statement came after the truth commission submitted its report on the violence to Yudhoyono, East Timor President Jose Ramos-Horta and East Timor Prime Minister Xanana Gusmao in Bali.

"We convey very deep regret at what happened in the past that has caused the loss of lives and property," Yudhoyono said.

Indonesian security and civilian forces had a major role in systematic, widespread "gross human rights violations," while a small number of East Timor's pro-independence groups also played minor parts in the violence, the report said. These violations included murder, rape and other forms of sexual violence, torture and illegal detention, it said.

It called on the two presidents to take moral and political responsibility to apologize to their people, especially the victims, for the suffering afflicted by their institutions during the conflict between pro-integration and pro-independence forces.

The commission said civilian officials provided funding and weapons to militia groups to intimidate, threaten and force people to vote for integration with Indonesia.

The report did not name perpetrators, but also did not recommend an amnesty. Several Indonesian military officials were tried in Indonesian human rights courts following the 1999 violence, but none were convicted.

Activists demand punishment

Rights activists said the two governments must continue the judicial process to try the perpetrators.

"The Indonesian government must reform its institutions, one of the ways is by punishing the perpetrators and making sure similar gross human rights violations will never happen again," said a statement by the HAK foundation, Human Rights Working Group and the International Centre for Transitional Justice.

David Cohen of Berkeley University, a commission adviser, said it was up to the international community to respond to the report, but questioned how much will there would be. An arm of the UN's human rights body said in 2005 the Security Council should hold an international trial.

"I don't think there's a political will of the Security Council to address the issue in a serious way so the question will be I think to what extent the international community accepts the decision of the two governments," said Cohen.

Rights groups have said they will push for a trial of retired General Wiranto, who faced an indictment by a special UN panel, under universal jurisdiction after the report is submitted. Wiranto, who was in charge of security at the time of the independence vote, has denied any wrongdoing.

Indonesia invaded East Timor in 1975, after Portugal abruptly pulled out of a colony it had ruled for three centuries, and annexed the territory later that year, maintaining a heavy and at times brutal military presence. (Editing by Ed Davies)