Indonesia and East Timor have accepted a report on violence that marred East Timor's vote for independence in 1999. Chad Bouchard reports from Jakarta.

During a meeting on the island of Bali, leaders of both countries expressed regret over violence following East Timor's independence vote, which ended 24 years of Indonesia's heavy-handed rule.

United Nations officials say about 1,000 East Timorese were killed during Indonesia's withdrawal from the newly independent state.

The commission's final report says Indonesian military and civilian groups had a major role in widespread gross human rights violations, including rape and torture.

Speaking after a brief ceremony in Bali, Indonesian President Susilo Bambang Yudhoyono said he conveyed very deep regret at what happened in the past. He said by helping to uncover the truth about the violence, the report lays a foundation for the two countries to work toward a lasting friendship.

He added that the focus of the report is on institutions, not individuals.

Human rights workers have criticized the commission, saying it lacks teeth and specifically blocks the report from being used to prosecute those responsible.

Critics also say its scope was too narrowly focused on violence around the 1999 referendum and does not delve into abuses going back to the start of Indonesian rule.

For those reasons, the UN boycotted the commission's work.

Spokesperson for the Indonesian Human Rights Committee, Maria Leadbeater, says in spite of the criticisms, the report exceeded expectations.

"The report has come out quite clearly with a statement of the responsibility for the crimes of 1999, as being laid directly at the feet of the Indonesian military, the Indonesian police, and Indonesian government officials," she said.  "And I think that's deeply significant."

Leadbeater and other human rights activists are calling for an international tribunal to follow up on the commission's report.

Harif Azhar with Kontras, a Jakarta-based human rights organization, says the report should be used as a starting point for future actions.

"They can make a recommendation strengthening the duty of states to prosecute the perpetrators," he said.  "To as soon as possible, to fulfill the victims' justice and victims' rights. To make a reform to institutions that's behind the crimes that happened in East Timor."

The two governments established the Truth and Friendship commission in 2005 to look into the violence.

The report does not recommend amnesty for those connected to the violence.

Several Indonesian military officials have been brought to trial for their part in the incident, but no one has been convicted.