The Commission for Reception, Truth and Reconciliation in East Timor (CAVR), an independent organisation established by the East Timorese Government, is calling for reparations for victims of torture, rape and violence perpetrated by Indonesia from its invasion in 1975 to its bloody withdrawal in 1999.
The 2500-page report, which President Xanana Gusmao presented to East Timor's parliament on Monday, contentiously recommends East Timor's victims be paid compensation by the colonisers Indonesia and Portugal, as well as by those nations that sold weapons to Indonesia and supported its annexation - including Australia.
Mr Gusmao spelled out the detail of the recommendation, and told parliament he was "truly concerned" by it.
The commission also recommended a continuation of the UN-backed investigation and prosecution of war crimes in East Timor during the Indonesian occupation.
"This recommendation does not take into account the situation of political anarchy and social chaos that could easily erupt if we decided to bring to court every crime committed since 1974 or 1975," Mr Gusmao said.
East Timorese and international activists condemned the President's stance, and demanded the immediate release of the full report, which has been put on hold indefinitely.
A hero of East Timor's guerilla war against Indonesia, Mr Gusmao has long signalled his determination to stay on good terms with Indonesia. A pragmatic leader, he has repeatedly said East Timor's future matters more than its past.
Part of the CAVR report says: "The Permanent Members of the Security Council, particularly the US but also Britain and France, who gave military backing to the Indonesian government between 1974 and 1999 and who are duty-bound to uphold the highest principles of world order and peace and to protect the weak and vulnerable, (should) assist the Government of Timor-Leste in the provision of reparations to victims of human rights violations suffered during the Indonesian occupation. Business corporations that profited from the sale of weapons to Indonesia during the occupation of Timor-Leste (should) contribute to the reparations program."
The commission, established in 2002 by the East Timorese Government, investigated the killings during the occupation, interviewing hundreds of people and compiling the first accurate estimates of the deaths.
In the report, the commission appealed to the international community to hand over those suspected of human rights abuses, freeze their assets and stop them from travelling as a prelude to a series of trials.
In a long and discursive statement to parliament, Mr Gusmao took pains to distance the Government from the commission's recommendations.
"The grandiose idealism that (the commissioners) possess is well manifested to the point that it goes beyond conventional political boundaries," he said.
The US-based International Centre for Transitional Justice has demanded the immediate release of the report in the pursuit of justice.
"After decades marked by suppression of the truth and impunity for human rights abuse, the immediate dissemination of the final report's findings and recommendations is essential," the organisation said.
"The commission's legal mandate to research and report the facts, contribute to victims' dignity and recommend measures to prevent future abuses cannot be discharged without publicising the final report."
Mr Gusmao is required to submit the final report to UN Secretary-General Kofi Annan, so its eventual release is inevitable. It is likely the President simply wants to forestall the criticism of Indonesia coming directly from East Timor.
Indonesia has prosecuted 18 soldiers, police officers, civil servants and civilians in connection with East Timor atrocities. In a judicial process widely condemned as a whitewash, they were all were found innocent, or their convictions were overturned on appeal.
Additional reporting: The Times