The gunbattle occurred after civilians reported cattle thefts to the military, Maj. Julieto Ando, spokesman of the Armys 6th Infantry Division, said.
When troops arrived on the scene, they encountered 20 armed men. Some of the gunmen took refuge in the villagers houses, resulting in the deaths of two civilians, including a six-year-old boy, and the wounding of three other people in the crossfire, Ando said.
After the armed men fled, troops recovered four rifles as well as documents and patches of the Moro Islamic Liberation Front (MILF), the countrys main Muslim separatist group.
The MILF signed a ceasefire with the government last year and is now engaged in talks but clashes with the military still take place.
Military officials accuse the 12,500-strong MILF of circumventing the ceasefire by sheltering criminal gangs engaged in kidnapping for ransom and banditry. John Unson, AFP