The clash broke out Tuesday near the town of Pangantucan on the main southern island of Mindanao, one of several areas where the decades-old New People's Army (NPA) rebellion is still active.
"It was really an ambush but our special forces returned fire," said local military spokesman Captain Alberto Caber, describing the rebel band as about 60-strong.
"There were reports of the NPA (in the area) so our special forces went there to verify," he told reporters.
The bodies of five guerrillas were recovered after the clash, he was quoted by AFP as saying.
The 4,000-strong NPA has for 46 years waged a guerrilla campaign which has claimed tens of thousands of lives, largely in rural areas mired in poverty.
Peace negotiations have stalled under President Benigno Aquino as the government has refused to grant the rebels' demand to free a number of their captured leaders, who face criminal charges.