From 2005 to 2008, Babo Soares, together with of Indonesia, co-chaired the Indonesia–Timor Leste Commission of Truth and Friendship (CTF), which was tasked with working on behalf of the Presidents of both countries in dealing with human rights violations during the 1999 East Timorese crisis. Pro-Indonesia militia and Indonesian security personnel had inflicted a wave of violence upon the occupied East Timor after the population had voted for independence in a referendum. Around 250,000 East Timorese had fled or been deported to West Timor, and around 2,000 to 3,000 people had died. The CTF's final report found that Indonesia's government, military and police were “to blame for the serious violations of human rights” in the 1999 crisis. Indonesia's President Susilo Bambang Yudhoyono then expressed his "very deep remorse at what happened in the past".