The violence on the island of Mindanao was spurred by police officers attempting to arrest members of a breakaway rebel organization, the New York Times reported.
The fighting and abduction occurred after a landmark peace deal was signed Saturday with the country's largest Muslim insurgency group, the Moro Islamic Liberation Front.
"There is no direct link between the signing of the peace agreement and this operation," Col. Ramon Zagala said in a phone interview. "But it has an effect on the peace process. We consider this group to be a spoiler to the peace agreement."
Two days after the peace deal was made, the police and military assaulted the Bangsamoro Islamic Freedom Fighters, a splinter rebel group opposed to the agreement.
"This was a law enforcement operation initiated by the government and led by the Philippine National Police," he said. "This is not your ordinary bandit group. They are well armed and well organized, so the Armed Forces of the Philippines were needed to support the police."
Thirty-seven rebels and one soldier were killed.
During fighting on the eastern side of the island, a government soldier and three rebels were killed in a battle Wednesday morning.
In a separate incident, eight armed men kidnapped a school district supervisor Monday.