It said air and artillery strikes by the government and its allies during their five-year siege of the Eastern Ghouta had deliberately targeted civilians in the town and destroyed its infrastructure, denying them access to food and medical treatment.
Despite the onslaught, a Syrian military source told Reuters news agency that more than 18,000 people were expected to stay in Harasta under government rule.
Another 2,000 people, including 600 to 700 rebels from the Ahrar al-Sham group, would leave for Idlib on 40 buses on Thursday, the source added.
On Wednesday, state media reported that a total of 1,500 rebels and 6,000 civilians were expected to be evacuated under the deal with the government.
What has happened so far?
The implementation of the deal began on Thursday morning with a prisoner swap.
State TV reported that 18 people were freed, 13 of them held by the rebels. It interviewed a soldier among them, who thanked God and the army for his release.
The BBC's Martin Patience in Beirut says the deal may put pressure on the rebel groups that control other parts of the Eastern Ghouta to follow suit.
Similar deals have been on the table with Jaysh al-Islam - which controls the northern pocket around Douma - and Faylaq al-Rahman - which controls the southern pocket around Arbin and Zamalka - but have yet to get anywhere.
Both factions have vowed to keep fighting, even as they have been driven further and further back.
Government air strikes killed at least 19 people on Thursday, according to the Syrian Observatory for Human Rights.
The UK-based monitoring group also said more than 4,000 civilians had fled Douma on foot and crossed into government territory through the al-Wafideen checkpoint over the past 24 hours. The civilians were leaving under an agreement between Jaysh al-Islam and Russia, it added.
Rockets and mortars are also still being fired by rebels into government-held districts of Damascus. A police source told Sana that two civilians were killed and four others injured by a shell that hit the Barzeh area on Thursday.