The Philippine Justice Department on Wednesday recommended murder charges against 90 Muslim rebels, even though such a move could jeopardise a peace process championed by President Benigno Aquino.

The department said the Muslim rebels could be charged over the January 25 incident which left 44 police commandoes dead in the rural district of Mamasapano.

"It was murder all the way and around," the report said, charging that members of the Moro Islamic Liberation Front (MILF), which agreed to a ceasefire with the government last year, and other Muslim armed groups had banded together to kill the commandoes who were on a mission in the strife-torn south.

This could affect the government's peace process with the 10,000-member MILF which is aimed at ending a four-decade old separatist struggle that has claimed an estimated 120,000 lives.

In a summary of its investigation, the Justice Department said MILF and other Muslim bands attacked the commandoes even though they knew they were policemen.

The report charged that the attackers continued to shoot the policemen even when "the latter already raised their arms in surrender.

"After the firefight, MILF elements crossed the river over to the cornfield to finish off the dying (policemen)," the summary added.

The Justice Department said it had to withhold the names of witnesses and suspects as this could make it difficult to make arrests.

The government peace panel, which hoped to seal a peace deal with the MILF before Aquino steps down next year, said they were studying the report and would issue a reaction.

The MILF has previously said it would not surrender men wanted in connection with the incident despite impending criminal charges.

"We maintain that our combatants involved in the Mamasapano incident defended themselves so they did that in self-defence. As far as we're concerned, they did not commit any crime," MILF vice chairman Ghazali Jaafar had said earlier.

Aquino had originally hoped to pass a law authorising an autonomous region for the nation's Muslim minority -- the key part of the peace pact, before the end of his term.

But outrage over the killing of the policemen has delayed the law's passage with numerous legislators now challenging it.

However Aquino said in an exclusive interview with AFP earlier this month that he still believed the law could be implemented during his term as opposition was now softening.

The raid apparently succeeded in killing an alleged top terrorist, Malaysian bomb-maker Zulkifli bin Hir, one of the United States' most wanted.

The Justice Department said further investigation was also needed into allegations that policemen had killed Muslim civilians and that the United States played a role in the botched raid.

Aquino has warned that failure to implement a peace accord could radicalise the MILF's moderate base and cause further bloodshed in the south of this largely Catholic nation.