The biggest Muslim rebel group in the Philippines signed an historic pact Thursday to end one of Asia's longest and deadliest conflicts, promising to give up their arms for an autonomous homeland.

Following four decades of fighting that has claimed tens of thousands of lives, the Moro Islamic Liberation Front (MILF) signed the peace deal with President Benigno Aquino's government at a high-profile ceremony in Manila.

"The comprehensive agreement on Bangsamoro is the crowning glory of our struggle," MILF chairman Murad Ebrahim said at the signing ceremony, using a local term that refers to a Muslim homeland.

"With this agreement the legitimate aspirations of the Bangsamoro and the commitment of the government of the Philippines to recognise those aspirations are now sealed."

The pact makes the MILF and the government partners in a plan to create a southern autonomous region for the Philippines' Muslim minority with locally elected leaders by mid-2016.

"What is being presented before us now is a path that can lead to a permanent change in Muslim Mindanao," Aquino said at the ceremony, attended by more than 1,000 people.

The Bangsamoro region would cover about 10 percent of territory in the mainly Catholic Philippines. The planned region has a majority of Muslims, but there are clusters of Catholic-dominated communities.

Muslim rebels have been battling since the 1970s for independence or autonomy in the southern islands of the Philippines, which they regard as their ancestral homeland dating back to when Arabic traders arrived there in the 13th Century.

The conflict has condemned millions of people across large parts of the resource-rich Mindanao region to brutal poverty, plagued by Muslim and Christian warlords as well as outbreaks of fighting that has led to mass displacements.

The conflict also created fertile conditions for Islamic extremism, with the Al-Qaeda linked Abu Sayyaf group and other hardline militants making remote regions of Mindanao their strongholds.

The MILF, which the military estimates has 10,000 fighters, is easily the biggest Muslim rebel group in Mindanao, and the political settlement was greeted with relief and optimism in the south.

"I am really happy. In the face of all the hardship of our parents, we the next generation hope and pray that Christians and Muslims will have peace," Mona Rakman, 42, a mother of four who lives close to the MILF headquarters, told AFP.

The autonomous region would have its own police force, a regional parliament and power to levy taxes, while revenues from the region's vast deposits of natural resources would be split with the national government.

It would have a secular government, rather than being an Islamic state. The national government would retain control over defence, foreign policy, currency and citizenship.

There are about 10 million Muslims in the Philippines, roughly 10 percent of the population, according to government statistics. Most live in the south of the country.

- Fragile peace -

However there are no guarantees the peace deal will be implemented by the middle of 2016, a crucial deadline as that is when Aquino is required by the constitution to end his six-year term.

Aquino needs to convince Congress to pass a "basic law" to create the Bangsamoro autonomous region, ideally by the end of this year to allow time for other steps such as a local plebiscite.

But even though Aquino enjoys record-high popularity ratings, there are concerns politicians could reject or water down the proposed law.

Powerful Christian politicians in Mindanao are regarded as potential deal breakers, while others elsewhere may see political advantage in opposing the deal to appeal to some Catholics ahead of the 2016 national elections.

The deal is also likely to be challenged in the Supreme Court, which in 2008 struck down a planned peace deal the MILF had negotiated with Aquino's predecessor, Gloria Arroyo.

Islamic militants opposed to the peace deal are another threat, and could continue to create enduring violence in Mindanao.

Among the potential spoilers is the Bangsamoro Islamic Freedom Fighters (BIFF), an MILF splinter group of a few hundred militants that has carried out deadly attacks in the south in recent years.

"We will continue to fight against the government of the Republic of the Philippines because we are for independence and nothing else," BIFF spokesman Abu Missry Mama told AFP by phone from his southern hideout.

The MILF leadership has committed to working with the government to neutralise the threat of the BIFF.

However the MILF will not give up its arms or the identities of its fighters until the basic law has been passed, highlighting the fragility of Thursday's peace deal.

In his speech, Aquino warned militant and political foes alike that he was prepared to crush any challenge to the peace deal.

"I will not let peace be snatched from my people again," Aquino said to applause.

"Those who want to test the resolve of the state will be met with a firm response based on righteousness and justice."