Syrian troops were pursuing small groups of rebels inside the historic Christian town of Maalula Thursday, a security source in Damascus said.
"The army continues to advance in Maalula to defeat the armed men," the source told AFP on condition of anonymity, describing "pockets of resistance," including snipers, inside the town.
He said recapture of the ancient town was difficult because of its geography -- the town is nestled in the side of a cliff, making it an easy target for those stationed above it.
The army entered Maalula on Wednesday after rebels, including members of the jihadist Al-Nusra Front, had seized the town several days earlier.
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State television broadcast images of military vehicles and troops inside the town, which was virtually deserted.
Most of residents have fled, with many taking refuge in the neighbouring Sunni town of Ain al-Tineh, and others travelling to Damascus, 55 kilometres (34 miles) away.
Picturesque Maalula is considered a symbol of the ancient Christian presence in Syria.
Its people are among the few in the world who speak Aramaic, the language of Jesus Christ.
The town, home to around 5,000 people, is strategically important for rebels, who are trying to tighten their grip around the capital and already have bases south and west of Damascus.
Maalula could also be used as a launching point for attacks on the highway between the capital and Homs, a key regime supply route.