There were no immediate reports of fresh fighting on Tuesday in the Mindanao region but military forces were strengthened in anticipation of fresh attacks.
A senior army general said military reinforcements had been deployed to prevent a repeat of Monday's carnage, when about 200-500 Moro Islamic Liberation Front (MILF) fighters cut off a main highway and raided up to five coastal towns in Lanao del Norte province.
The military said 26 civilians and eight soldiers were killed in Monday's fighting in Kolambugan and Kauswagan towns.
Dozens of civilians were used as human shields and some of them were shot dead by retreating fighters, according to the military.
Monday's attack was the bloodiest since a territorial deal with the MILF stalled earlier this month and comes just days after government troops halted an offensive against MILF fighters in another part of Mindanao.
The MILF leadership has distanced itself from the latest attacks, saying that renegade commander Abdullah Macapaar, also known as Bravo, ordered them without the knowledge of the group's leadership.
"We regret the loss of lives and property in Lanao del Norte, but we would to emphasise that the MILF leadership has not authorised these actions," spokesman Eid Kabalu said, adding that the MILF remained committed to peace and that Macapaar would "face the consequence of his action".
But General Yano countered that the MILF leaders had no control over their field commanders.
"If they can't control them, the government will certainly control them and we will undertake our mandate to protect the people and the communities and we cannot renege on that constitutional mandate," he said.
In Iligan, Lanao del Norte's provincial capital and industrial centre of 300,000 people, the authorities imposed a 10pm-5am curfew and suspended schools due to bomb threats and the unstable security situation.
Last week, the military bombed MILF positions for four straight days, triggering an exodus of around 160,000 people, after accusations that the separatists had occupied Christian-owned farmlands.
Stalled peace plan
The MILF has been waging a 30-year guerrilla campaign for a separate Islamic state in the south of the largely-Christian Philippines - a conflict that has killed over 120,000 people.
The separatists signed a ceasefire with the government in 2003 to open the way for peace talks, and both sides said in July they had completed a draft agreement for recognition of MILF's "ancestral domain" in the south.
However, the agreement on the size of a Muslim homeland and a future government's powers, including rights over exploring and developing mineral reserves, oil and gas, was halted amid protests by local Catholic politicians in Mindanao.
The Supreme Court suspended the draft accord, raising new tensions, earlier this month and the situation on the ground has deteriorated rapidly since then.
Hawks on both sides have seized on the stalling of the peace moves to re-ignite fighting that has been mostly dormant since 2003.
Mohaqher Iqbal, the chief rebel negotiator, has said that if nothing comes out of the current peace process with the government, the separatists will return to war.