The Philippine president has warned that the collapse of a peace deal with the country's largest Muslim rebel group would lead to a new wave of violence, after criticism of the accord followed the killing of at least 44 police commandos in the southern island of Mindanao.

President Benigno Aquino III called on Wednesday for continued support for the pact with the Moro Islamic Liberation Front (MILF), but added he also expected MILF to help authorities identify the rebels who killed the elite police commandos.

"If the peace process were derailed, how many more graves would we have to dig?" Aquino asked in a national television address.

The Muslim autonomy deal signed last 2014 stands to be one of the legacies of Aquino, whose six-year term ends next year.

Aquino was treading on delicate grounds when he spoke about the police killings in the southern province of Maguindanao - the government's biggest single-day combat loss in recent memory.

Aquino came under fire when a newspaper report revealed that he was aware of the police operation, but failed to coordinate with the military and the rebel representatives as required by the ceasefire agreement.

Lingering questions

A representative of the MILF rebels told Al Jazeera that they were unaware of the operation, and that they acted in "self-defence" when they fired back against the police commandos.

However, questions remain why the clashes went on for at least 12 hours.

Al Jazeera has learned that at least two of the police commandos killed were Muslims from the southern city of Zamboanga, but many came from other areas, including northern Philippines.

Legislative hearings are under way to pass a law governing the new autonomous Muslim region. 

"If this law is kept from being passed at the soonest possible time, the peace process will be derailed," Aquino said.

He cited a decision by at least two senators to withdraw support for a proposal in the peace deal to establish a more powerful autonomous region for minority Muslims in the south of the predominantly Roman Catholic nation.

"If that happens, we cannot hope for anything but the same results: Citizens who take to the mountains after losing hope. ... It would be as if we helped Marwan and Usman to reach their goals," he said, referring to the top Malaysian and Filipino suspects who were targeted in Sunday's police raid, in a territory controlled by the rebels.

Commitment pledged

Marwan, has been identified as a leader of Jemaah Islamiyah, Southeast Asia's largest al-Qaeda affiliate. Usman is a commander of the MILF splinter group Bangsamoro Islamic Freedom Fighters (BIFF).

The US has offered $5m for Marwan's capture, and $2m for Usman.

Al Haj Murad, MILF leader, said his 11,000-strong armed group remained fully committed to the peace pact, and added that his group is investigating the clash.

"An enduring peace and justice remain to be our primary objective," Murad said.

"It is unfortunate but not entirely surprising that when parties do not follow established protocols lives are placed in harm's way."

Mujiv Hataman, regional governor, called on government and MILF not to let Sunday’s clash derail the peace process.

“We must guard the gains in the ongoing peace process,” he told Al Jazeera.

Aquino's peace agreement with the MILF have virtually ended major fighting in the south in the last four years. The decades-old Muslim separatist insurrection has left at least 120,000 people.

With additional reporting by Ferdinandh Cabrera in Cotabato City

Source: Al Jazeera and agencies