Philippines President Rodrigo Duterte has put his weight unequivocally behind efforts to bring a negotiated end to more than four decades of conflict in the south of the country, but uncertainty is bleeding momentum from the process and the clock is ticking.

The Duterte administration inherited a peace process that had stalled when Congress failed to pass enabling legislation that would have created an autonomous region for Muslims in key parts of Mindanao and the southern islands. The proximate cause of the political resistance in Manila was a botched police raid on a radical splinter group in January 2015 in which 44 policemen died, but there were other problems including questions over the constitutionality of some of the provisions and the fact that the negotiating process had been dominated by a single southern group, the Moro Islamic Liberation Front (MILF).

President Duterte is making good on his campaign promise to push the process forward. He has promised to abide by the deals signed by the Aquino administration; appointed a close confidante from his Davao days, Jesus Dureza, to run the process; and reached out to other groups, particularly the leader of the other main Muslim insurgent group, Nur Misuari of the Moro National Liberation Front, who has a long history of disagreement with MILF.

But there is less clarity now than there was at the end of last year. The government’s push for greater inclusivity by inviting MNLF, indigenous peoples and other constituencies into the process is in principle beneficial – if successful it will ensure greater buy-in to the finished deal – but there is a possibility the new participants could insist on re-negotiating from scratch, leading to substantial and dangerous delays. The negotiations should use the Comprehensive Agreement on Bangsamoro, the deal agreed in 2014 between the government and MILF as the framework for the failed enabling legislation, as the starting point for the new discussions.

Government negotiators have suggested to Crisis Group that they may be willing to split an autonomous Bangsamoro in two, with MILF de facto running the portions on Mindanao and MNLF running the islands of Basilan, Sulu and Tawi-Tawi. This would be a retrograde step that would both undermine the economic viability of the new entity and necessitate lengthy discussions of the modalities of collaboration between the two groups.

There is also uncertainty as to how the process will fit in with Duterte’s ambitious plan to change the Philippines into a federal state. Government negotiators have suggested that Bangsamoro autonomy could act as a template for federalism. They say that the more constitutionally controversial aspects of the southern dispensation could be parked until the constitution is overhauled to make way for federalism. This would be an invitation for opponents in Congress to water down any legislation to a level that would be unacceptable to the Moro population.

None of these problems are insurmountable, but they will take time to solve and it is unclear how much time there is before the security situation begins to deteriorate significantly.

There are three threats to a successful conclusion. The first is President Duterte’s ability to push the legislation through. At present he is almost unchallenged in Congress, but his agenda has upset a broad range of vested interests and it would be naïve to think that they will not strike back. Derailing a headline initiative like the Bangsamoro legislation would be an attractive way of weakening Duterte while hiding behind professions of patriotism

The second threat is disaffection in the South. MILF members say, and there is no reason to doubt them, that they and their armed cadres are fully committed to the peace process, but they have only conditional support from Moro youth. There have been at least three main peace agreements between Manila and the insurgents, starting with the 1976 Tripoli accord, none of which have delivered a sustainable peace. There is a strong narrative in Bangsamoro that they have been serially betrayed by Manila, and the problems in the current process have fed that skepticism.

Should they finally lose faith in this round, there is a danger that they will feed the already growing trends of anarchic criminality, most likely in conjunction with already well established clan-based criminal gangs, or fall victim to jihadi radicalisation.

Crisis Group research indicates that much of the success of jihadi groups elsewhere in the world has been due to their ability to exploit disorder of the sort that might be triggered by a prolonged hiatus, let alone a collapse, in the peace process.

The seeds of radicalisation are already there. A number of groups, including the Abu Sayyaf faction led by Isnilon Hapilon based in Sulu, have pledged allegiance to Islamic State, and there is evidence of an emerging threat from university students radicalised online.

Under normal circumstances, the threat would probably be real but limited. The central identity of the insurgents is ethno-nationalist rather than religious; Abu Sayyaf is regarded by most in the south as a criminal enterprise specialising in kidnap and ransom for profit; and there are significant cultural barriers to jihadi-salafi interpretations of Islam – when Indonesian militants have fled to the area, they have hardly been given a heroes welcome.

But the third threat is external. Islamic State’s hold over its territories in the Middle East is becoming more tenuous; the head of IS, Abu Omar al-Baghdadi has already mentioned the Philippines as one of the group's key international conflicts; and a Syria-based Malaysian, Mohammed Rafi Uddin, has called on militants who can’t make it to Syria to converge on Hapilon and his Abu Sayyaf faction.

Should IS implode, a flood of angry South East Asian militants could head back to the region bringing with them the skills and cash that could provoke a step change in violence.

Crisis Group believes that the best bulwark against these threats is a rapid delivery of enabling legislation that is substantial enough to address the key aspirations of the Moro people. But even in the best-case scenario, this will take time and there are a number of measures that will help to both stave off a crisis and boost preparations for eventual autonomy.

The government should deliver an early peace dividend in the shape of development funds for infrastructure, agriculture and health. The funds should be delivered through mechanisms that include MILF, MNLF and other local constituencies. This would boost their legitimacy and relevance, and improve their ability to control fissile forces within the Moro Community.

The government and the international community should use the opportunity of the hiatus to boost local technical capacity. If an autonomous Bangsamoro is to have control of taxation and investment, for example, it will need bureaucrats versed in developing investment policy and running excise systems.

And finally the government should run a nationwide public awareness campaign to mitigate the damage of four decades of anti-Muslim propaganda. This would both weaken opposition to the passage of the bill and improve the chances of a strong and constructive relationship between an autonomous south and the rest of the Philippines.

The Philippines is closer to peace today than at any point in the last four decades. If it can successfully navigate the next few months and deliver a sufficient degree of autonomy to the south, the impact on local, national and regional peace and prosperity will be significant. But if it fails, the situation is unlikely to go back to the status quo ante: the future will be more unpredictable, and potentially much more violent.

Photo by George Calvelo/Anadolu Agency/Getty Images