The gunmen, who oppose the main Islamic rebel group's negotiations with Manila, ambushed an army truck on the main southern island of Mindanao, regional military spokesman Colonel Dickson Hermoso said.
Two soldiers were wounded in the initial volley, but the army gave chase to the retreating gunmen and killed five of them, he said in a written report.
The pursuit also left two soldiers dead and four other soldiers wounded, Hermoso added.
The group had mounted attacks on Mindanao on July 6, two days before the government resumed peace talks with the region's main rebel group, the Moro Islamic Liberation Front.
The earlier fighting had left five soldiers and three gunmen dead and sparked fears that it would affect the peace talks.
The military however ended its pursuit of the renegade rebel force before the talks resumed in Malaysia on Monday.
The peace talks aim to create an autonomous region for the Muslim minority in Mindanao, the southern third of the mainly Catholic nation of 100 million.
The Kuala Lumpur talks aim to spell out revenue-sharing terms with the national government in the self-rule area.
The talks were continuing today, President Benigno Aquino's spokeswoman Abigail Valte said in an interview on government radio.
The 12,000-member MILF has waged a guerrilla war for a separate Islamic state in Mindanao since the 1970s that has claimed an estimated 150,000 lives.
The BIFF is led by Ameril Umbrakato, a Saudi Arabia-trained cleric who was expelled by the MILF in 2011 for his hardline stance against the peace talks.
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