Conflict and displacement affecting Philippines' minority groups continued during the first year and a half of Benigno Aquino III's presidency, both as a result of militarization and natural disaster. The Moro Islamic Liberation Front (MILF), a major armed Islamic group, is currently engaged in peace negotiations with the government. The Mindanao region, home to a significant number of Muslim Moro or Bangasmoro, has seen a long-running struggle with armed insurgency groups seeking autonomy in the majority Christian Philippine state. Negotiations resumed in February 2011. While an agreement was reached in December to create a functioning autonomous government for the Moros, negotiations are ongoing and will have to address the rights of minorities within Moro territory, a major cause of the breakdown in talks in 2008.

Mindanao is also the ancestral territory of indigenous groups, collectively known as Lumad.

In northern Cordillera, in the Luzon region, a variety of heterogeneous indigenous groups are collectively referred to as Igorot. Indigenous groups in the Mindoro region of the Vasayas are collectively called Manygyan. Many indigenous communities across the country have been drawn into the conflict between the central government and the New People's Army (NPA) – the armed wing of the Communist Party of the Philippines (CPP) that has been fighting for over four decades for a communist take-over. Communities have been accused of supporting the NPA and targeted by anti-insurgency operations of the Armed Forces of the Philippines (AFP). In February, the government resumed negotiations with the CCP-NPA in Oslo for the first time in six years. But talks stalled later in the year.

Both human rights defenders from indigenous communities and those supporting their rights have been targeted for extra-judicial killings, threatened and harassed throughout the Philippines. During Aquino's first 18 months in office, the National Alliance of Indigenous Peoples in the Philippines (KAMP) recorded 13 indigenous rights activists killed, at least 4 of whom were resisting mining in their communities.

The AFP has long been implicated in these and other politically motivated killings over the last decade. Rudy Dejos, a B'laan indigenous community leader in Santa Cruz, Davao del Sur, was killed in February 2011 along with his adult son. According to HRW, Dejos' body showed signs of being tortured. He had previously been threatened by the AFP; the police blame the NPA, but his family is not convinced.

Conflicts relating to mining concessions in Moro and indigenous peoples' lands continued throughout 2011. The Xstrata-controlled Sagittarius Mines-proposed open-pit gold and copper mine in Tampakan, South Cotabato drew particular controversy. The company intends to push forward its application despite evidence of lack of free, prior and informed consent on the part of affected B'laan communities, as well as a province-wide ban on open-pit mining that was declared in 2010. The company claims it has the backing of local communities, while activists question whether those who support the project understand its environmental consequences. The mine will straddle the territory of four ancestral domains of the B'laan indigenous people. The project has led to a string of violent incidents in 2011, including the murder in February of a S'bangken indigenous leader who supported it. The NPA has attacked the mine in the past and warned of further violence if the project proceeds.

In January, Aquino instituted a counter-insurgency programme, the Oplan Bayanihan (OB), ostensibly to foster peaceful relations between conflict-affected communities and the military. KAMP has argued that it only increases militarization in indigenous areas. In October, the NPA attacked three mining operations in Surigao del Norte, killing three private security guards and damaging equipment. In response, the government agreed to allow mining companies to hire militias to protect their sites. A statement released by the Special Committee of the Koronadal Indigenous Peoples Women Gathering, an indigenous women's coalition, said: 'This sounds like a blanket call to intensify attacks against us.' According to KAMP, 60 per cent of the total land area of the Cordilleras has been approved for mining applications and operations. Indigenous communities in Pampanga and Cagayan Valley also contend with the massive influx of large-scale mines.

In November, the Internal Displacement Monitoring Centre (IDMC) reported that 34,000 people remained displaced following separate instances of heavy fighting between the AFP and MILF, as well as suspected renegade MILF groups, in October in Basilan and Zambonga Sibugay provinces. Drawing on UN Office for the Coordination of Humanitarian Affairs (OCHA) findings, the IDMC reported a total of 46,000 displaced at that time.

On 17 December, tropical storm Washi hit northern and south-western parts of Mindanao. By January 2012, over 1,200 had died in the flash floods. The devastation was exacerbated by deforestation, leading the Autonomous Region of Muslim Mindanao's (ARMM) recently appointed governor Mujiv Hataman to declare a logging ban in ARMM, at the behest of the central government.

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