"Units from our heroic army have made major advances, chasing down terrorists from Al-Nusra Front in the town of Maalula," said an official cited by state news agency SANA.
The army "has made it across the town's main square and has reached the Mar Takla convent," said the source, adding that "dozens of terrorists have been wiped out".
The regime has used the word "terrorist" to its opponents ever since the start of an uprising against President Bashar al-Assad's rule in March 2011.
A security source earlier told AFP that "the army has not yet retaken Maalula" and that fighting between rebels against troops was "raging on".
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The army's advance comes a day after rebels announced they would withdraw from Maalula, but that this was "conditional" on pro-regime forces not taking their place.
"The army and its shabiha (militias) must not enter into the town," a spokesman for the rebels said in an online video statement.
"To ensure no blood is spilt and that the properties of the people of Maalula are kept safe, the Free Syrian Army announces that the town of Maalula will be kept out of the struggle between the FSA and the regime army," he said.
A nun from Mar Takla convent in Maalula told AFP by telephone that "there were fierce battles (on Tuesday) but the town was not shelled. We and the orphans we take care of are doing well, but we lack fuel".
The town, home to about 5,000 people, is strategically important for rebels, trying to tighten their grip around Damascus and who already have bases circling the capital.