MANILA (REUTERS) - The largest Muslim rebel group in the Philippines handed in 16 assault rifles taken from police commandos killed in a January firefight that has jeopardised milestone peace talks, in what the group said on Wednesday was a show of goodwill.

The Jan. 25 firefight on the southern island of Mindanao between the Moro Islamic Liberation Front (MILF) and members of the police Special Action Force has thrown the talks into doubt and left President Benigno Aquino facing a political crisis.

Forty-four police commandos were killed in the fighting, the first clash between Philippine security forces and the MILF in about four years.

The 12-hour firefight, the result of a botched operation to capture an al Qaeda-linked bombmaker, left embarrassing questions for Mr Aquino to answer about why a police officer suspended over corruption allegations was involved in planning and executing the raid.

A public outcry over the deaths of the commandos heaped pressure on Aquino to abandon a peace deal with the MILF and seek retribution for their deaths.

On Tuesday, international peace monitors and peace negotiators from the government and the MILF went to a marshland village in the heartland of MILF territory in Mindanao for the return of the weapons.

Mohagher Iqbal, head of the MILF peace negotiating team, said the MILF had tracked down the weapons and returned them to show its sincerity and commitment to the peace process. "We are partners in this process," Iqbal told a news conference at a southern army base.

He said he hoped it would also convince legislators to pass a law setting up a new Muslim autonomous government in the area. Congress has suspended deliberations on the bill until an inquiry into the deadly raid is finished.

Mr Aquino's peace adviser Teresita Quinto Deles described Tuesday's ceremony as "a gesture of trust and goodwill".

"The peace process has been disrupted, but not beaten back,"she said.

About 50 weapons and other equipment taken from police in the ambush are still missing. The two sides signed the peace deal in March 2014 to end 45 years of conflict that has killed more than 120,000 people, displaced 2 million and stunted growth in the poor but resource-rich areas in the south.