MANILA » The Philippine president and a Muslim rebel leader secretly met last week and helped resolve thorny differences over a proposed autonomy law that threatened to stall efforts to end decades of rebellion in the south, officials and the insurgents said Monday.

President Benigno Aquino III and Al Haj Murad Ebrahim of the Moro Islamic Liberation Front agreed to endorse a draft of the proposed legislation after meeting for more than two hours at the presidential palace Thursday, presidential adviser Teresita Deles said.

Aquino will submit the bill to Congress on Wednesday, bringing efforts by the government and the 11,000-strong insurgent force to end one of southeast Asia’s longest-raging Muslim insurgencies a step closer. The rebellion has killed thousands and hampered progress in a resource-rich frontier region that is home to minority Muslims in this largely Roman Catholic nation.

The government and the Moro insurgent group, the largest of at least four in the south, signed a new deal in March that aims to establish a more powerful and potentially larger Muslim autonomous region to be called Bangsamoro. Under the deal, the rebels agreed to eventually disband their guerrilla forces in exchange for broader autonomy.

Differences, however, threatened to stall the drafting of the autonomy bill.

Aquino’s top aides met behind closed-door with rebel commanders to try to patch up differences, including the extent of power and territory of the Muslim region and wording of the draft legislation. The president and Murad met to resolve the final issues.

"It was like a championship boxing match," said rebel negotiator Mohagher Iqbal. "And there are more bouts to come."

Deles, however, said both sides have committed to overcome major disagreements.

Several Asian and Western governments, including the United States and the European Union, have backed the Malaysian-brokered peace process in the south partly to prevent the Muslim insurgency from becoming a sanctuary of foreign extremists.

In 2008, the government and the rebels were close to signing a preliminary peace deal but Christian politicians questioned the legality of the pact, which eventually fell apart, igniting rebel attacks. Major fighting resumed, killing scores of people and displacing tens of thousands of villagers.