The evacuation comes after an apparent auto bombing that targeted a bus convoy carrying people to safety in the Rashideen area, near Aleppo.
Around 2,220 evacuees from two rebel-held towns - Madaya and Zabadani - were similarly blocked at a transit point in government-held territory, one of them told AFP by telephone.
Rami Abdurrahman, who heads the Britain-based Syrian Observatory for Human Rights, and Hezbollah's Al-Manar TV said 3,000 people were to be evacuated from Foua and Kfarya, while 200, the vast majority of them fighters, were to be evacuated from Zabadani and Madaya.
UN Secretary-General Antonio Guterres has strongly condemned today a terrorist attack in Syria against a convoy of buses evacuating 5,000 civilians and armed opponents who made a decision to leave their terrorist-besieged towns.
There has been no claim of responsibility for the attack.
Pope Francis yesterday also urged an end to the war in Syria as he presided over the traditional Easter mass in Rome.
The convoy was carrying at least 5,000 people including civilians and several hundred pro-government fighters, who were granted safe passage out of the two Shi'ite villages which are besieged by rebels.
In the latest deal, hundreds of rebels and their families evacuated the town of Madaya near Damascus, and were taken to the regime-held city of Aleppo.
About 100 people were killed Saturday April 15 in a vehicle bomb explosion targeting pro-regime evacuees leaving besieged Syrian towns, a volunteer rescue agency said.
The rebel group Ahrar al-Sham tweeted that some of its members died in the blast.
"We're sad and angry about what has happened", he said. He added it was not clear how many rebels were killed because they were evacuated to their areas.
The Syrian Civil Defense organization, known widely as the White Helmets, said their volunteers had counted 100 bodies, which included children, women, and rebel fighters.
A previous attempt at mutual evacuations failed in December when rebels burnt coaches due to be sent to the towns.
The Shiites have reached the rebel-held town of Rashideen, while the rebels have reached the government-controlled Ramouseh crossing in Aleppo. Most of the victims were believed to be residents of two Shi'ite villages that had been surrounded by Islamists for months. "I condemn it and call for those responsible to be brought to justice", he said in a statement.
Critics say the string of evacuations, which could see about 30,000 people moved across battle lines over the next 60 days, amounts to forced displacement along political and sectarian lines.