"An elderly couple and their adult son were killed by the rebels," he said.
The story was much the same in other areas of the province as the MILF fighters left burning houses and crops in their wake.
The military said at least 27 fighters were killed and nine wounded with one soldier dead and 12 wounded.
Felizardo Serapio, the regional police chief superintendent, said: "The operations are over. We are just clearing up.
"Houses have been razed and scattered gun fire and mortar shelling is still going on as the rebels retreat," he said.
Philippine troops regained control of two villages in clashes on Monday that killed at least one soldier and seven MILF separatists.
The Philippine military pounded rebel Muslim positions on Sunday, shooting off a barrage of artillery and mortar fire and firing rockets from helicopters at suspected separatist positions in North Cotabato province after hundreds of separatists refused to leave Catholic farmlands they have occupied since last month.
Clashes in the region between the fighters and government forces have displaced nearly 160,000 people.
The civil defence reports that 159,123 people have fled their homes in 56 villages in the province, many of them to evacuation centres.
Lieutenant-General Cardozo Luna, the military vice-chief of staff, said the military operation, involving more than 2,000 troops, was not directed against MILF in general, but a group headed by MILF commander Umbra Kato, who is no longer following the orders of the group's main leadership.
|The MILF has been fighting a decades-long war for an Islamic state [EPA]
"The MILF rebels have defied their own leadership and have refused to leave the area," he said.
He said they were supposed to have complied with a government deal with the MILF leadership to move out of the disputed areas, but "they just re-positioned and occupied other villages".
The violence is the worst seen since the supreme court halted plans to establish an extended Muslim homeland in the southern Philippines last week.
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 Catholic politicians.
The 12,000-strong MILF has been waging a 30-year guerrilla campaign for a separate Islamic state in the south of the largely-Christian Philippines.
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.