Arroyo's statement coincided with a rise in military operations, particularly in the central islands, carried out by rebels of the New People's Army, NPA.
About 30 soldiers and militiamen have been killed and 13 others wounded in clashes with the communists in recent weeks, authorities say.
"The response to the violence is our launch of comprehensive countermeasures where we will simultaneously use military, political and legal action to fight this group," Arroyo said in a radio speech.
"We are combining all necessary measures to stop this threat and defeat it by the use of force, political action and long term social reforms," she added.
But the president did not provide details on what measures will be used.
The president said she would also take up the growing influence of the NPA in hinterland villages during a tour of the central islands of the Philippines in the coming week.
"I want to know what their problems are there, why are they turning to the NPA, a group which claims to fight for democracy but really seeks to topple the government through violence," Arroyo said.
The NPA is the armed wing of the Communist Party of the Philippines (CPP), which has been waging a Maoist rebellion in the countryside since 1969.
Arroyo suspended peace talks with them two years ago after the rebels gunned down two legislators.
The future of peace talks with another rebel group, the Moro Islamic Liberation Front (MILF) is in doubt after the government made it clear negotiations would be sidetracked if the group was found to be responsible for Thursday's bombing in Koronadal.
Bomb forensics experts have found evidence linking the blast in the southern Philippines to similar explosions in the region, Defense Secretary Angelo Reyes said on Saturday.
The device that went off in Koronadal, killing three people, left the same residue as two other bombs that went off in the southern city of Davao in March and April, killing about 40 people, Reyes said.
The bomb blasts in Davao were blamed on the MILF.
But Reyes said he could not conclude the MILF was behind the attack until investigations were complete.
The MILF has denied involvement in the bombings in Koronadal and Davao, two predominantly Christian cities.
The MILF is fighting for a separate Islamic state in the southern Philippines.