The soldiers were on the central island of Negros yesterday investigating reports that New People's Army guerrillas were extorting money from villagers when they clashed with about ten rebels, leaving three soldiers dead and two wounded, a military report said.
The violence comes just days after President-elect Rodrigo Duterte said he was open to resuming peace talks aimed at ending a decades-old insurgency that has claimed tens of thousands of lives.
After his May 9 election victory, Duterte's spokesman said the firebrand politician may release jailed communist rebels in an effort to reopen peace talks.
Duterte, a hardline mayor accused of running vigilante death squads that have allegedly killed more than a thousand crime suspects in the Southern city of Davao, is a friend of Netherlands-based Jose Maria Sison, who set up the communist party in 1968.
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Duterte, who takes office on June 30, has previously described himself as a socialist.
Running for almost half a century, the communist insurgency has claimed 30,000 lives, according to military estimates.
However it retains support among the deeply poor in the rural Philippines.