Rebels led by al-Qa’ida-linked fighters gained control of a Christian town north-east of the capital, Damascus, Syrian activists said on Sunday, while government media continued to claim that regime forces were winning.

Maaloula, strategically located in the mountains overlooking Damascus, is a Unesco World Heritage Site, hailed as a beacon of Christianity and one of the last places in the world where the ancient language of Aramaic is spoken. The Muslim population has grown in recent decades, and the two religions frequently wage a war of words over loudspeakers, Friday prayers from the town’s two new mosques competing for attention with hymns of nuns that reverberate through the valley.

Now, the town has fallen into a far more violent back-and-forth as government forces have battled to regain control from the al-Qa’ida-linked Jabhat al-Nusra rebels, who first overran government roadblocks and entered the town last Wednesday.

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Most of the civilian population fled as pro-government news outlets vowed that the military would “liberate” the town.

Government forces entered the town on Saturday morning, leading to fierce clashes throughout the day, “but they left when rebels started pouring into the village”, said Rami Abdul-Rahman, a spokesman for the British-based Syrian Observatory for Human Rights.

He said that Jabhat al-Nusra was backed by another group, the Qalamon Liberation Front, which moved into the town after heavy clashes with the army late on Saturday. He said around 1,500 rebels are inside the town.

“The army pulled back to the outskirts of the village and both [rebel groups] are in total control of Maaloula now,” Mr Abdul-Rahman said.

Mother Pelagia Sayah, the head of Saint Tekla monastery in Maaloula, denied earlier reports that churches and monasteries had been attacked. But the recent kidnappings of prominent Orthodox bishops, plus the Christian peace activist Father Paolo Dall’Oglio, have raised disturbing parallels to the height of sectarian violence in Iraq, and fears that Syria’s Christian minority may not survive the war.

The siege of Maaloula comes as tens of thousands of Christians around the world gathered to pray for peace in Syria. The Pope led a five-hour prayer session in St Peter’s Square in Rome. In Damascus, too, hundreds followed his lead, while the Syrian clergy implored Christians to remain in the country. “I beg you to remain here,” the Melkite Greek Catholic Patriarch Gregory III Laham was reported as saying. “We’re staying. If you leave, we leave. So we beg you, stop coming to our priests asking for a visa. If you leave, who will remain? Only our brethren the Muslims.”