Chris McCall – Aceh's prayers for peace have not been answered despite a landmark deal to halt the violence that has ravaged the Indonesian province.

The agreement signed in Geneva yesterday between Jakarta and the Free Aceh rebels was a milestone, but stumbling blocks remain, particularly whether the de facto ceasefire will hold. A Malaysia-based rebel leader rejected the deal before it was even signed and insiders say there are serious fears within Indonesia's military that it could lead to their withdrawal from the province.

Free Aceh, also known by the acronym GAM, insists it has not given up its demand for an independent Islamic state, something the military has vowed to prevent.

"This is a step forward, however small. It may enable the humanitarian situation to improve," said Saifuddin Bantasyam, executive director of Care Human Rights Forum, a top human rights monitor in Aceh. "But I have the impression that the military does not want there to be a dialogue with GAM. In truth, there has been no meaningful change in the intensity of the conflict. The battle is still between GAM and the Indonesian military and police."

Sources close to the talks say that if the deal works, police may ultimately be expected to conduct joint security operations with guerillas, a tall order since this year's death toll includes 38 police and soldiers. Police stations have become prime bombing targets in a wave of attacks spread across virtually the entire province of 3.5 million.

Key issues – including when and if a referendum on independence might be held – have been skirted. Neither have the rebels said whether they would consider autonomy within Indonesia as an interim solution. But the main body campaigning for a referendum welcomed the deal, despite its limitations.

Despite a series of public statements by the military backing the deal, insiders say it insisted that the word "ceasefire" be left off. The top brass appear afraid to give away too much ground, fearing the exposure of the true nature of the largely secret war in the province before former president Suharto's downfall in May 1998. "They don't want disarmament," a source close to the talks said.

Leading Indonesian human rights group Kontras has outlined a series of follow-up measures it sees as necessary, including disarmament, the formation of an investigative team into past human rights abuses and an agreement on the future relationship between Aceh and Jakarta.

The conflict had been largely seen as unsolvable amid fears that independence for Aceh would trigger a messy break-up of the whole of Indonesia. Most leading Acehnese believe a referendum would result in a vote for independence, but many doubt it would be a resounding victory as in East Timor.