Violence continued to plague the southern region of Mindanao, home to most of the country's minority Muslim community, after a breakdown in peace negotiations between the government and the Moro Islamic Liberation Front (MILF) the previous year. A ceasefire was declared on 29 July 2009, but fighting was ongoing in some areas. In May 2009, the National Disaster Coordinating Council reported that there were still 703,949 internally displaced persons (IDPs), most of whom were Muslim. Living conditions were poor in evacuation centres, which lacked sufficient food, water and sanitation. Diseases are common and some IDPs have died due to lack of medical attention. The military reportedly blocked relief supplies to IDPs, who were publicly labelled as an 'enemy reserve force' by Lt. Col. Jonathan Ponce, spokesman for the sixth infantry division, during a 30 June 2009 forum, according to the Asian Legal Resource Centre, an NGO.

Another armed group, Abbu Sayyaf, continued to mount attacks in 2009 and carried out kidnappings against civilians. The most publicized incident was the 15 January kidnapping on the island of Sulu of three representatives of the International Committee of the Red Cross. They were freed in April and October. On 10 and 11 April, Abbu Sayyaf members allegedly killed two farmers in Zamboanga City; the group claimed that the farmers were members of a Christian militia, according to IRFR 2009.

As a signatory to the UN International Convention on the Elimination of All Forms of Racial Discrimination, the Philippines came under review during 2009. In the 28 August 2009 report released by the committee overseeing the convention, committee members expressed concern that 'leaders of these communities continue to be victims of extrajudicial executions as well as of disappearances and detention and over reports indicating occupation of indigenous territories by the armed forces and armed groups'. The committee was also concerned about 'the effects of internal displacement as a consequence of armed conflict especially on indigenous peoples'. The newspaper Davao Today reported on 5 March that members of the Lumad indigenous people in Mindanao were being forcibly recruited by the military to fight the New People's Army, a communist rebel group.

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