Indonesia’s president acknowledged his country carried out gross human rights abuses during East Timor’s 1999 break for independence, but stopped short of offering a full apology Tuesday for murders, torture and other crimes.

A bilateral truth commission, set up in 2005 to investigate the bloodshed, said Indonesian soldiers, police and civil authorities engaged in an “organized campaign of violence” against independence supporters.

Indonesia should apologize for the immeasurable pain and suffering caused, the commission said in a 300-page report presented Tuesday to President Susilo Bambang Yudhoyono and his East Timorese counterpart, Jose Ramos-Horta.

“We convey our deep regret over what happened,” the Indonesian leader said after signing a joint-statement accepting the commission’s findings and expressing “remorse.” “Let us not forget those who were victimized during this dark period in our past.”

East Timor voted overwhelmingly to end 24 years of often-brutal Indonesian rule in a 1999 referendum that triggered a burst of killing, looting and burning by Indonesian soldiers and their militia proxies that killed at least 1,000 people.

Only one Indonesian has ever been jailed in connection with the violence.

The commission, set up to head off demands by human rights groups for a U.N.-backed tribunal to try those responsible for the violence, does not name individuals responsible for the violence or make provisions for prosecutions.

Yudhoyono said the intention was only to uncover the truth so that the two sides could move forward in promoting friendship and reconciliation.