The rebels raided shops and banks, and burned houses down
Extra troops have been deployed in the southern Philippines, a day after separatist rebel raids on several towns left about 30 people dead.
Hundreds of Muslim rebels attacked towns in Lanao del Norte on Monday, looting shops and burning houses.
A spokesman for the Moro Islamic Liberation Front (MILF) said a renegade commander was to blame for the attacks.
The violence came after the Supreme Court blocked a land deal aimed at ending years of fighting in the south.
The government had agreed to expand an existing Muslim autonomous zone on Mindanao island.
But the court suspended the deal earlier this month after Christian communities argued it would increase sectarian divisions.
Two weeks ago rebels occupied villages in North Cotabato province. The military used air strikes and artillery assaults to force them back and casualties were reported on both sides.
Monday's raids in Lanao del Norte province took place near the border of the existing autonomous zone.
In pre-dawn attacks, rebels attacked at least two towns and some outlying villages. Troops and police fought fierce battles with the rebels in the mostly Christian towns of Kolambugan and Kauswagan.
About 30 civilians and troops were killed and some residents were taken hostage by the retreating guerrillas, reports said. Several thousand people fled the fighting.
Philippine military chief Gen Alexander Yano said troops would chase down the rebels.
"You all know we have bent as far backward [as possible] to give peace a chance," he told local radio.
"The patience of our soldiers in trying to uphold the primacy of the peace process is very commendable but at some point we really have to act decisively."
He accused the MILF leadership of having no control over local commanders. "If they can't control them, the government will certainly control them," he said.
Troops are now searching for the rebels, who are thought to have escaped into nearby forest areas. A night-time curfew has been imposed in Iligan, the provincial capital of Lanao del Norte.
More than 100,000 people have been killed in almost four decades of separatist fighting in the south.
The Philippine government had hoped that the autonomy deal would kick-start talks with the rebels.
The Supreme Court is scheduled to hold another hearing on the agreement on 22 August.