The framework peace agreement unveiled on Sunday by the Philippines government and the main southern Muslim insurgent group, the Moro Islamic Liberation Front (MILF), is a feather in the cap of President Benigno Aquino after 15 years of on-off talks and failed ceasefires, and may significantly boost regional security. But the autonomy deal faces a long, obstacle-strewn road to final implementation in 2016 and is certain to be challenged by splinter groups and terrorist gangs in Mindanao and by Aquino's political opponents in Manila.

In bullish mood, Aquino stressed the prospective economic benefits that peace would bring to a region that is home to a treasure trove of largely untapped natural resources, including oil, gas and minerals. "This framework agreement paves the way for final and enduring peace in Mindanao. 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," he said.

If the deal really does bring an end to the violence, the beneficial effects may be felt far beyond the southern Philippines. The majority Muslim population of Mindanao – the Philippines as a whole is predominantly Roman Catholic – has been caught up in a separatist struggle spanning the past 40 years that is said to have claimed the lives of 120,000 people.

In recent years, al-Qaida-linked terrorist groups seeking regional sway, such as Abu Sayyaf in Mindanao and mainly Indonesia-based Jemmah Islamiyah (JI), sought to recast the conflict as a jihad to create an Islamic caliphate. Their trail of bombings, kidnapping, beheadings, and destabilisation and infiltration operations ranged from Mindanao to Bali, Aceh, and Jakarta in Indonesia, Malaysia and southern Thailand. As long as it continued, the Mindanao conflict provided bases and fuel for this holy fire.

In January 2012, the Philippines military said it had killed two key JI leaders in a raid in the south – Malaysian Zulkifli bin Hir, or Marwan, one of the region's most-wanted militants, and Mohammad Ali, alias Muawiyah. The US was alert to the threat, framing the insurgency as part of the "global war on terror". Special forces were sent to Mindanao to support Filipino troops against Abu Sayyaf.

Abu Sayyaf is now said to be reduced to 400 militants in total, but both it and JI can be expected to do whatever they can to undermine the Mindanao deal. So, too, may splinter factions that have broken with MILF's leader, Al Haj Murad Ibrahim. One rebel commander, Ameril Umbra Kato, formed a new 200-strong group last year specifically opposed to the peace process. His forces launched a string of attacks on army camps in August. More trouble is likely from that quarter.

MILF's renunciation of the goal of independence and repudiation of terrorism paved the way for today's breakthrough. But its followers have not renounced armed struggle, remain armed to the teeth, and like broadly similar movements, for example in Northern Ireland, the Spanish Basque country and south-east Turkey, could quickly regress or fall out with each other if the peace process does not bring dividends quickly. In fact, history may be repeating itself. In 1996 the Moro National Liberation Front signed a peace deal that did not include disarmament. The pact foundered when a rejectionist faction broke away to form what is now the MILF.

Aquino will also face opposition closer to home, as next May's mid-term congressional and gubernatorial elections loom. Politics in the Philippines is a passionate and sometimes violent business dominated by powerful family clans, political dynasties, and celebrity figures. Those lining up their 2013 candidacies include the former first lady Imelda Marcos, her daughter Imee,and the former president Joseph Estrada, who was kicked out of office by a "people power" revolt in 2001 after previously vowing to crush the MILF in an "all-out war". Another former president, Gloria Macapagal Arroyo, was arrested last week on corruption charges.

Aquino's plan may struggle to survive this torrid, turbulent arena. And again, there is a discouraging precedent. In 2008 a similar preliminary autonomy pact was declared unconstitutional after political opponents petitioned the supreme court. In place of peace an upsurge in violence ensued, displacing 750,000 people and leaving more than 100 dead.