Members of an air force combat unit ran into about 30 New People's Army (NPA) rebels, an armed unit of the Communist party, while patrolling near the town of Calatagan in Batangas province south of Manila, triggering the clash on Tuesday.
There were no casualties on the government side, but two armed men were killed and two others wounded and captured, military spokesman Lieutenant-Colonel Buenaventura Pascual said.
The Calatagan gun battle came a day after NPA rebels killed two airport policemen outside an airport in eastern Catanduanes province, and a day after the Philippines was rocked by a series of three bombs blamed on the al-Qaida linked Abu Sayyaf group.
In Monday's attack the NPA rebels ambushed the policemen responding to the attack, killing a third officer and wounding seven others. A civilian was also killed in the crossfire.
The Communist Party of the Philippines last year suspended peace talks with the Manila government.
Monday's explosions in the capital Manila and on the Mindanao island claimed many lives.
Two more people died from injuries suffered in the explosions bringing the number of people killed in the Valentine's Day bombings in three Philippine cities to 12, according to an updated police toll, which listed 136 people as injured.
An explosion in Davao City was
part of the 14 February killings
The number of those killed when a bomb rigged to a tricycle exploded outside a shopping mall in the southern city of General Santos on Monday has risen to five, police said.
In Davao City on the southern island of Mindanao, one person was killed when a bomb exploded in a bus terminal while in Manila's financial district a bomb on a bus killed six people and injured scores of others.
The Philippine government on Tuesday offered 500,000 pesos ($9260) as a reward for any information leading to the arrest of members of the Abu Sayyaf group accused of being behind the bombings.
As security in the main installations across the country was stepped up, national police chief Edgardo Aglipay appealed to the public for calm as he announced the reward.
"We are offering 500,000 pesos for information that will lead to their arrest," Aglipay said.
After Monday's attacks, Arroyo vowed to wipe out the Abu Sayyaf group.
"More than ever, we must not pull back, but move forward to wipe out the remnants of the Abu Sayyaf," she said in a statement on Tuesday.
Arroyo has vowed to wipe out
the Abu Sayyaf group
"The evil of terrorism has only one aim. It is to rule with absolute power and absolute force. The desperation of the enemy cannot be underestimated, even as it lies in the throes of defeat."
Security around airports, ports, bus terminals, shopping malls and foreign embassies was tightened amid fears that Monday night's bombing campaign may be part of a wider, coordinated effort by the group.