The Philippine president has pledged justice for the families of 44 police commandos killed during a botched anti-terror operation, that has threatened to derail a peace deal with Muslim rebels.

President Benigno Aquino III promised grieving relatives on Friday that government forces would capture suspected bomb-maker Abdul Basit Usman, who escaped during Sunday's operation.

The 44 men were killed in confrontations with two rebel groups in the southern Philippines on Sunday, 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.

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

"As a president, even if I want to get mad, I cannot allow myself to be driven by emotion," he added. "I cannot make careless decisions. If I allow anger to dominate, rather than resolving the problem, we will just worsen it."

Botched operation

According to officials, the commandos were on a mission to catch or kill Malaysian bomb-maker Zulkifli bin Hir, who is accused of involvement in the 2002 Bali bombings in Indonesia that killed 202 people.

Hir, a suspect in at least nine bombings in the south, was apparently killed during the January 25 operation. Officials said a DNA test was still needed to confirm his identity.

Abdul Basit Usman, a suspect in at least nine bombings in the south, escaped the fighting.

Although Philippine forces have battled Muslim rebels for decades, the commandos' deaths have caused public outrage and tested the government's peace deal with the rebels, which was signed last year.

Several politicians have questioned the rebels' sincerity and at least two have withdrawn support from a pending law to implement an agreement granting minority Muslims autonomy in exchange for peace in the southern Philippines.

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.