The more than 2,000 page report was compiled over three years by an independent Truth and Reconciliation Commission. It chronicles widespread torture and use of napalm by Indonesian security forces that left more than 100-thousand East Timorese dead between 1975 and 1999.
The commission said another 80,000 died from hunger as the result of a deliberate Indonesian campaign of starvation and sexual violence.
East Timor's President Xanana Gusmao delivered the report Friday to U.N. Secretary-General Kofi Annan. He was accompanied by the country's foreign minister Jose Ramos-Horta.
Afterward, President Gusmao told reporters he saw the report as a way to heal the wounds of the past.
"The essential (thing) is to remind our future generations, not to commit all that happened, before, again, in East Timor. And we accept the result of the report as a way to tell the truth of what happened, as a way to heal the wounds of the people, minds in the people, even in the people's bodies. We need this. If we hide the truth, we will not be courageous enough to look at the other, eye to eye. That is why I believe that it is not so important to look at the figures, but it is more important to look at the lessons," he said.
President Gusmao pointed to South Africa as a model for reconciliation, and said "we do not advocate punitive justice but restorative justice".
The Truth and Reconciliation Commission said Indonesian forces and pro-Indonesian militias were responsible for 85 percent of the 100,000 deaths. Another 10 percent were blamed on pro-independence groups led by Mr. Gusmao.
Indonesia's government Friday denied many of the charges contained in the Commission's report. News agencies quoted Indonesia's Defense Minister Juwono Sudarsono as saying it would have been impossible for troops to have used napalm because, in his words "we didn't have the means to import, let alone produce" it.
Indonesia annexed East Timor in 1975 and imposed a brutal regime that ruled the former Portuguese territory until a forced independence vote in 1999. After the vote, The United Nations dispatched a peacekeeping force and administered the region until it became independent in 2002. That mission is scheduled to close down in May.