The violence comes ahead of the next round of peace talks between President Gloria Arroyo's government and the Moro Islamic Liberation Front (MILF) in Malaysia next month.
Both sides are expected to sign a peace treaty to end the
decades-old separatist movement at the end of the year. It was not immediately clear what impact the deaths would have on the peace process.
Three MILF guerrillas disguised as ordinary passengers boarded a minibus near the town of Midsayap on Mindanao island on Monday and shot dead two members of a government militia force, the army said on Wednesday.
The guerrillas escaped with the victims' rifles and bullet clips.
In a second attack on Mindanao on the same day, about 40 MILF guerrillas raided a village near the town of Ampatuan and abducted two militia members whom they later shot dead.
The army said it would submit a protest to the joint committee monitoring the July 2003 ceasefire with the MILF.