The more than 2000-page report, compiled by the Commission for Reception, Truth and Reconciliation (CAVR), established that at least 102,800 Timorese, roughly 10 per cent of the territory's current population, died as a result of the Indonesian occupation.
The presentation on Friday to the UN secretary-general was the fruit of more than three years of intensive work during which more than 7000 victims testified on human rights violations committed in East Timor between April 1974 and October 1999.
Speaking to reporters after his talks with Annan, Gusmao said the main objective of the report was to establish the truth of what happened and to ensure that the international community acts so that it does not happen again.
"We accept the results of the report as a way to heal the wounds," he said. "The figures can be disputed. But it is not so important to look at the figures. It is more important to look at the lessons.
"We don't advocate punitive justice but restorative justice," Gusmao said, citing South Africa, where a truth and reconciliation commission exposed the brutal excesses of apartheid and for the first time gave mainly black victims a voice, as a model.
Lessons to learn
The US-based East Timor and Indonesian Action Network (ETAN) urged the UN to publicise and discuss the findings in a bid to prevent a repeat of what happened in East Timor elsewhere and help find justice for the victims.
John Miller, ETAN's national coordinator, said in a statement: "Widespread understanding of the truth commission's report and recommendations is essential in charting a course of justice for victims."
The CAVR report blamed the deaths, most of them due to hunger and illness, on the policies of Indonesia's military toward East Timor's civilian population.
The Indonesian security forces "consciously decided to use starvation of East Timorese civilians as a weapon of war", the report said.
CAVR had submitted its report to the East Timorese government months ago, but Gusmao kept it secret until now for fear of irritating Indonesia, its powerful neighbour.
Indonesia annexed East Timor with the tacit approval of major powers but the brutality of the occupation turned world opinion against Jakarta and led to a vote for independence in 1999.
The vote sparked bloody reprisals by Indonesian-backed militia groups which killed hundreds of people before an international force restored order.
East Timor became independent in 2002 and remains Asia's poorest country.