Indonesia has formally expressed regret for the violence surrounding East Timor's vote for independence in 1999, in which more than 1000 people were killed.
President Susilo Bambang Yudhoyono said on Tuesday it was necessary to learn from the past. But he stopped short of a full apology.
Both Mr Yudhoyono and East Timorese President Jose Ramos-Horta have formally accepted the final report of a Truth and Friendship Commission, which followed three years of investigations.
The report details systematic crimes against humanity - and lays much of the blame at the door of Indonesia's army.
The commission was boycotted by the United Nations, which has demanded that those responsible face justice.
Both Mr Yudhoyono and East Timorese President Jose Ramos-Horta formally accepted the report, which followed three years of investigations.
Until now, Indonesia's official position has been that the human rights abuses committed in East Timor in 1999 were isolated incidents - the random acts of individuals.
East Timor voted for independence after 24 years of Indonesian occupation.