One of the world's longer, bloodier but least known internal conflicts could finally end after the president of the Philippines announced a groundbreaking deal with a Muslim rebel group that has spent 40 years battling for independence in the country's south.

Benigno Aquino said his government and the Moro Islamic Liberation Front (MILF) had come to a framework agreement under which the insurgent group would abandon an armed battle for independence and instead work on establishing an autonomous region in a mainly Muslim part of Mindanao, one of the island groups that form the predominantly Catholic country.

Negotiations have run intermittently for 15 years in an attempt to end the conflict, which has killed more than 120,000 people, displaced around 2 million and crippled development in the south of the Philippines, a country whose wider economy has grown rapidly in recent years, albeit from a low base.

When the bloodshed has been reported internationally it has mainly been through the actions of Abu Sayyaf, a hardline Islamist split-off from the MILF, which has periodically kidnapped and sometimes beheaded western tourists and missionaries, as well as local Christians.

In a televised announcement, which followed lengthy talks in Malaysia, Aquino said the agreement "paves the way for final and enduring peace in Mindanao". He continued: "This means that the hands that once held rifles will be put to use tilling land, selling produce, manning work stations and opening doorways of opportunity."

The deal, to be formally signed on 15 October, sets out the broad outlines for a new region called Bangsamoro, which would enjoy considerable autonomy, with Manila retaining control over defence, foreign policy and broad macro-economic policy. The MILF will be tasked with helping create a new "basic law" for the region, with final agreement scheduled for 2016, the end of Aquino's term as president.

The deal was welcomed by the US and UK, among others, with the British foreign secretary, William Hague, saying it had "the potential finally to end the long-running conflict".

Risks remain: in 2008 the Philippines' supreme court decreed another agreement unconstitutional, beginning a new wave of clashes that saw 750,000 people displaced. There is also the possibility of disruption from hardline splinter groups.

The MILF itself came into being in the 1980s, when another group, the Moro National Liberation Front, agreed on autonomy rather than independence. The MILF's main negotiator said the 11,000-strong group's fighters would not lay down their arms until the agreement was finalised.

However, the head government negotiator, Marvic Leonen, told the Guardian the MILF leadership appeared "principled but pragmatic". He said: "Of course, there are other armed groups on the ground but the agreement also has a section on how there can be co-operation between government and MILF troops to maintain peace in the area. There has been a ceasefire between the MILF and the government and, as far as we know, this year there have been zero skirmishes between them."

Kristian Herbolzheimer, Philippines programme director for Conciliation Resources, a London-based NGO that was part of international efforts to assist the negotiations, said the deal was a "very good framework" for lasting peace. He said: "This is probably the biggest milestone of the last 15 years of negotiations. At the same time, of course it's not the end point. This is a framework agreement, a road map of what has to follow. In Mindanao, of course, there have been several 'final' agreements which did not end the conflict."

Both sides made significant concessions, he said: the MILF in agreeing to autonomy rather than independence and the government conceding that a new framework for greater self-government in Mindanao had to be shaped by the rebel group. This placed trust in the MILF to bring into the fold dissenting voices.

He said: "It's a huge responsibility on the MILF's shoulders right now. They will lead this drafting process and they will have to prove to the Bangsamoros and the Filipinos that they are not sectarian and can reach out even to those who think differently."

If it comes into being, Bangsamoro will be a significantly deprived region of around 4 million people, with many investors likely to be put off by poor infrastructure and the potential for violence. However, this could change with the exploitation of significant oil and gas fields in the Sulu Sea off Mindanao.