KUALA LUMPUR, Malaysia >> The Philippine government and the country’s largest Muslim rebel group completed talks today on a deal to end four decades of fighting that has killed tens of thousands of people and helped foster Islamic extremism in Southeast Asia.

The accord between Filipino negotiators and the rebel Moro Islamic Liberation Front calls for Muslim self-rule in parts of the southern Philippines in exchange for the deactivation of the rebel force. Military presence in the proposed autonomous region would be restricted.

Much now will depend on how the accord is enforced, in particular whether the 11,000-strong rebel forces are able to maintain security in areas that would come under their control. At least four other smaller Muslim rebel groups are still fighting Manila’s rule in the southern Mindanao region, and could act as spoilers.

Officials from both sides announced the conclusion of talks in Kuala Lumpur in Malaysia, which has brokered the years-long negotiations. The accord and three other pacts signed last year make up a final peace agreement that is to be signed in the Philippine capital, Manila, possibly next month, presidential spokesman Edwin Lacierda said.

“This will give the just and lasting peace that our brothers in Mindanao are seeking.” said Lacierda, referring to the volatile southern region and homeland of minority Muslims in the predominantly Roman Catholic nation.

Chief government negotiator Miriam Ferrer said that concluding the talks “marks the beginning of the bigger challenge ahead, which is the … implementation.”

Saturday’s accord has been the most significant progress made over 13 years of negotiations to tame a tenacious insurgency that has left more than 120,000 people dead and derailed development in Muslim-populated southern regions that are among the most destitute in the Philippines.

The United States and other governments have supported the talks, worried that rebel strongholds could become breeding grounds for al-Qaida-linked extremists who have sought sanctuary in the region in the past.

U.S. Secretary of State John Kerry issued a statement congratulating both sides “for concluding negotiations toward an historic, comprehensive peace agreement.”

“The agreement offeres the promise of peace, security, and economic prosperity now and for future generations in Mindanao,” Kerry said.

Under the peace deal, the Moro insurgents agreed to end violence in exchange for broader autonomy. An existing five-province Muslim autonomous region is to be replaced by a more powerful, better-funded and potentially larger region to be called Bangsamoro.

Despite the milestone, both the government and the rebels acknowledged that violence would not end overnight in a region that has long grappled with a volatile mix of crushing poverty, huge numbers of illegal firearms, clan wars and weak law enforcement.

One rebel group vowed to keep fighting.

“We will continue the struggle,” said Abu Misri, spokesman of Bangsamoro Islamic Freedom Movement, which broke off from the Moro Islamic Liberation Front three years ago. “What we want is an Islamic state, an Islamic people, an Islamic constitution,” he told The Associated Press by telephone Saturday.

Rebels from another group, the Moro National Liberation Front, took scores of hostages in September when they seized coastal communities in southern Zamboanga city after accusing the government of reneging on its commitments under a 1996 autonomy deal. Thousands of troops ended the 10-day uprising with a major offensive that killed more than 200 people, most of them insurgents.

The accord Saturday outlined the gradual “decommissioning” of the rebel forces, some of whom could be absorbed into a regional security force. Another pact concluded involved the extent of control the proposed autonomous region would wield over resource-rich waters like the Sulu Sea.

Chief rebel negotiator Mohagher Iqbal said the latest accord “is the most sensitive, emotional and, as far as I know, it entails a lot of sacrifices on the part of the (rebels) because to pay for real peace in Mindanao we have to decommission our forces.”

He said their weapons will be “put beyond use” under an arrangement to be overseen by an International Decommissioning Body.

Evan Jendruck from the IHS Jane’s Terrorism and Insurgency Centre said the success of the new peace agreement hinges on the ability of the former Moro insurgents to put other armed groups under control. While the military would still have a presence in the new autonomous region, security would basically be in the hands of a Bangsamoro force composed of former insurgents.

“Will MILF be able to fill the power vacuum? If they don’t do that, then the peace process won’t go forward,” Jendruck said.

Iqbal said the peace process would not end with the signing of a peace accord. He said that a government-rebel council still needed to complete drafting a law creating the new autonomous region. The legislation then needed to get approval from Philippine Congress, where it is expected to come under intense scrutiny.

Despite the optimism, “let me caution ourselves this early that the final destination of this journey of peace is not within immediate reach yet,” Iqbal said.

A preliminary peace accord that was about to be signed in Malaysia was turned down in 2008 by the Philippine Supreme Court, sparking rebel attacks on Christian communities that provoked a major military offensive and shattered a cease-fire.

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Associated Press writers Jim Gomez and Oliver Teves in Manila, Philippines and Chris Brummitt in Hanoi, Vietnam contributed to this report.