The reciprocal evacuations from two pro-government villages and two opposition-held towns resumed under tight security.
The evacuation and transfer of thousands of Syrians from four besieged areas resumed on Wednesday, according to the UK-based Syrian Observatory for Human Rights (SOHR).
The reciprocal evacuations from two pro-government villages and two opposition-held towns was disrupted by a bombing on Saturday that killed more than 120 people.
A large convoy of buses from the government-held towns of Foua and Kefraya reached the edge of the rebel-held transit point of Rashidin outside the city of Aleppo.
"The process has resumed with 3,000 people leaving Foua and Kefraya at dawn and nearly 300 leaving Zabadani and two other rebel-held areas," the head of the SOHR, Rami Abdel Rahman, told the AFP news agency.
The Syrian government’s Central Military Media also confirmed the resumption of evacuations.
Rashidin was the scene of Saturday’s deadly car bombing. At least 109 of the 126 dead were evacuees, among them 68 children. The rest were aid workers and rebels guarding the convoy.
Security was tightened up for Wednesday’s departures. Several dozen armed rebel fighters stood guard over the marshalling area where the buses were parked.
When Wednesday’s evacuations are complete, a total of 8,000 people should have left Foua and Kefraya, including pro-government fighters as well as civilians.
In exchange, 2,500 civilians and rebel fighters should have left rebel-held areas, including the towns of Zabadani and Madaya near Damascus that are surrounded by pro-government forces.
The deal to evacuate the towns was the latest in a string of such agreements, touted by the government of Syrian President Bashar al-Assad as the best way to end the fighting. Rebels say they have been forced out by siege and bombardment.
The population exchange has been criticised by rights groups, which say it rewards siege tactics and amounts to forced displacement.
The deal, currently in its first stage, has been repeatedly delayed.
A second phase is due to begin in two months’ time which should see the two government-held towns entirely emptied and all fighters, and civilians who choose to, leave the two rebel-held towns.
In total, that will amount to more than 30,000 people.
There was no immediate claim of responsibility for Saturday’s bombing.
The Syrian government blamed "terrorists" - a catch-all term for its opponents. Ahrar al-Sham, a key rebel group in Syria’s north, condemned the "cowardly" attack, saying that many of its members were killed in the blast. The group said it was willing to cooperate with an international probe to determine the culprits.
The United Nations says 4.72 million Syrians are in hard-to-reach areas, including 600,000 people under siege, mostly by the Syrian army, but also by rebels or the Islamic State of Iraq and the Levant (ISIL) group.
There has been a series of evacuations in recent months, mostly around the capital Damascus but also from the last rebel-held district of Syria’s third city Homs.