More than 30 Philippine police commandos have been killed in a clash with fighters from the Moro Islamic Liberation Front (MILF) while hunting a top criminal suspect in the country's south, a local official has said.

Tahirudin Benzar Ampatuan, the mayor of Mamasapano, town told the AP news agency that dozens of police special action force members entered the village of Tukanalipao at dawn on Sunday to capture a bombing suspect.

As they entered the village, the police encountered and clashed with the MILF fighters in exchanges which lasted for 12 hours, the mayor said.

Ampatuan said some villagers entered the scene of the battle after the fighting subsided and retrieved at least five of the dead.

It was the biggest single-day combat loss for Philippine forces in many years.

The MILF, the largest rebel group in the south, accepted an autonomy offer from the government in March 2014, ending 45 years of conflict in which 120,000 people were killed and two million displaced.

Under the deal, brokered by Malaysia, the fighters were to surrender their weapons and disband after the government had set up a new autonomous government in the south and granted the Muslim minority wider economic and political power.