Operating over three years, the commission gave its final report on July 15, 2008, and presented it to the Presidents of Indonesia and East Timor, concluding that "gross human rights violations in the form of crimes against humanity did occur in East Timor in 1999" and that "pro-autonomy militia groups, TNI, the Indonesian civil government, and Polri must all bear institutional responsibility", as well as stating that "from a moral and political perspective the respective states must accept state responsibility for the violations identified in the report." The commission also made recommendations that both nations begin institutional reform enhancing the strength of investigative and prosecuting bodies involved with investigations into the events, as well as forming joint security policy to ensure the safety of individuals in case of the recurrence of violence. It also noted the need to resolve other standing border and security issues between the two nations to allow for more cooperation. Notably, the report gave no recommendations of amnesty or rehabilitation. The report was endorsed by the president of Indonesia, Susilo Bambang Yudhoyono, making it the first recognition of the Indonesian government's complicity in human rights violations in East Timor by Indonesia.
