A long, slow procession of coffins draped in the Philippine flag poured out of military transport planes in Manila on Thursday, as the country mourned dozens of policemen killed in a botched anti-terror operation.

Borne by uniformed colleagues marching to muted drums, the numbered coffins had been flown to an air base in the capital from the southern island of Mindanao, the scene of the worst loss of life by the country's police or troops in recent memory.

Philippines president Benigno Aquino has declared Friday a day of mourning for the 44 police commandos who were slaughtered in a cornfield when their top-secret mission - to kill or capture one of the world's most wanted Islamic militants - went badly wrong.

The killings have sparked growing calls for retribution. Analysts warn this threatens the peace process aimed at ending a decades-long armed conflict that has claimed tens of thousands of lives in impoverished Muslim regions of the mainly Catholic Philippines.

Relatives wept and hugged each other at the air base as a priest sprinkled holy water on the caskets, which were laid in front of a large national flag at half-mast. Cabinet ministers and politicians watched from the stands.

"As president and as father of this country, I am greatly saddened that our policemen had to lay down their lives for this mission. Without question, these people are heroes," Mr Aquino told the nation on Wednesday.

The president was absent from Thursday's ceremony, attending another public event.

His spokeswoman Abigail Valte denied suggestions that the president snubbed the arrival honours, telling reporters he was set to attend memorial services for the dead at a police camp in suburban Manila later on Friday.

Two of the slain officers have already been buried by their Muslim kin.

Fate of terror-raid targets unknown

Almost 400 police commandos had swooped before dawn in the operation to hunt down Zulkifli bin Hir alias Marwan, a top suspect in the 2002 Bali bombings and one of the United States' most wanted militants, with a $US5 million bounty for his capture.

But after killing a person they thought to be Zulkifli, the commandos came under devastating ambushes by at least two large guerrilla groups.

Mr Aquino said most of the casualties were sustained after they ran into the Moro Islamic Liberation Front (MILF), which signed a peace treaty with Manila last year, and the Bangsamoro Islamic Freedom Fighters, who are allied to Islamic State fighters in Iraq and Syria.

Police say Zulkifli was killed in the operation, although there has been no independent confirmation of his death. Mr Aquino said a second target, Filipino militant Abdul Basit Usman, escaped.

The MILF maintains that it acted in self-defence and has vowed to pursue the peace process.

To cement the peace, Mr Aquino has urged wavering politicians to pass a proposed law granting regional self-rule to Muslim regions in time for the end of his six-year rule in mid-2016.

But senators have warned the law is now unlikely to be passed by March as planned.

AFP