Abdulrahjak Kabalu Siambal, 31, believed to be an MILF commander, and Marcos Ruta were killed instantly when gunmen on a motorcycle attacked them in the town of Polomolok, Chief Inspector Florendo Quidilla said.
Witnesses said that the attackers, wearing helmets that covered their faces, pursued Siambal and Ruta and shot them dead, Quidilla said.
The motive for the attack was unclear, Quidilla added, declining to say if the killing might be linked to the Muslim insurgency.
The 12,000-strong MILF is the country’s largest remaining Muslim guerrilla force and has been fighting for the establishment of an independent Islamic state in Mindanao since 1978.
It entered into a ceasefire with the government in 2001 to pave the way for peace talks, but sporadic clashes between the military and MILF guerrillas in remote areas have persisted.
Last Sunday, a MILF peace negotiator, Edoh Abdulah, was killed by a lone gunman outside the residence of MILF vice chairman for political affairs Ghadzali Jaafar in Isulan, Sultan Kudarat.
Police said the attack on Abdulah, commander of the MILF’s 104th Command based in Sultan Kudarat, might have been due to a personal grudge.