Philippine President Benigno Aquino delivers a speech in front of the caskets of slain members of the Special Action Force (SAF) who were killed in Sunday's clash with Muslim rebels, during a service inside a police headquarters in Taguig city, south of Manila, on Friday. 

AFP/Manila

Philippine President Benigno Aquino pledged justice for the families of 44 police commandos killed by Muslim rebels during a botched anti-terror operation, as he led tributes on Friday - a national day of mourning.

The men were killed in confrontations with two rebel groups in the southern Philippines on Sunday while on a mission to catch or kill Malaysian bomb-maker Zulkifli bin Hir alias Marwan, who is accused of involvement in the 2002 Bali bombings in Indonesia in which 202 people died.

"I feel your pain," Aquino told weeping widows, parents and children of the police commandos at an emotional memorial service inside a police camp in suburban Manila.

"I pledge to bring justice to all those who were killed," said the president, sporting the same black armband worn by police attending the ceremony.

An awkward silence, broken only by the sound of infants crying, filled the cramped gymnasium as Aquino personally offered his condolences to victims for the first time since the massacre, praying briefly before each white casket.

In his eulogy, Chief Superintendent Noli Talino repeated a Philippine government claim - not yet independently verified - that Zulkifli was killed by a small assault force that crept up to his hut before dawn.

"Is it worth it? (Is) one international terrorist equivalent to 44 Special Action Force troopers. If you will ask them - it is worth it," Talino said, his voice breaking.

Aquino was attacked by many for failing to attend a parade ceremony on Thursday that saw uniformed commandos bearing the coffins of their fallen comrades as they arrived home in Manila.

The president chose to attend the opening of a Japanese car assembly plant instead.

Aquino vowed on Friday that one of his government's top priorities would be to go after Philippine militant Abdul Basit Usman, who has been accused of at least nine bombings in the south of the country.

Police said earlier Usman had escaped the scene.

The 44 men lost their lives in firefights with large units of Filipino Muslim rebels who surrounded them, according to officials, including the Moro Islamic Liberation Front (MILF), which signed a peace agreement with Manila last year.

The MILF maintains that it acted in self-defence and has vowed to pursue the peace process, as it seeks regional self-rule.

It has denied military claims in the past that it was giving shelter to Zulkifli and other foreign militants and letting them train MILF members in bomb-making.

The other group officials say attacked the policemen is a MILF splinter group called the Bangsamoro Islamic Freedom Fighters (BIFF), which last year pledged allegiance to Islamic State fighters in Iraq and Syria.