A group of soldiers were ambushed by rebels in Quezon province, about 150 kilometres southeast of Manila, local spokesman Lieutenant Colonel Oliver Maquiling said, leaving a lieutenant and a regular soldier dead and four others wounded.
He said that the soldiers had been on a "medical mission" and blamed the New People's Army (NPA) for the attack.
"They just wanted to help people through this medical mission," Maquiling said. "This was not a combat mission. We condemn this action of the NPA."
The military had braced for retaliatory attacks since the arrest on Saturday of Communist Party of the Philippines (CPP) chairman Benito Tiamzon and his wife, the party's secretary general Wilma Tiamzon.
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Benito Tiamzon had overseen the NPA, the CPP's military wing which once numbered more than 26,000 in the late-1980s but has shrunk to about 4,000.
However the NPA remain a threat, frequently ambushing small military and police units and extorting money from rural businesses.
Military spokesman Lieutenant Colonel Ramon Zagala said the latest attack was part of the rebels' "regular tactical offensives" and was likely not related to the Tiamzons' arrest.