The agreement is the latest in a string of evacuation deals, which the government of President Bashar Assad says are the best way to end the violence after more than six years of civil war.
The Syrian Civil Defense in Aleppo province, also known as the White Helmets, said their volunteers pulled at least 100 bodies from the site of the explosion.
There has been no claim of responsibility for the attack which pro-Damascus media said was carried out by a suicide auto bomber. It is not clear who was responsible for the bombing, but Sunni jihadist groups, including the Syrian affiliate of al-Qaida, operate in the area and routinely attack Shi'ites, whom they consider apostates.
The Britain-based Syrian Observatory for Human Rights said Sunday about 120 buses and ambulances have made their way into Foua and Kfaryam to assist with the population transfer to Aleppo.
"They were residents of two besieged Shia minority villages, who'd been besieged by rebels for years".
According to the same source, in his Easter Sunday address, Pope Francis condemned the attack, calling it "an ignoble attack on fleeing refugees".
Earlier on Saturday, at the transit point where the buses from al-Foua and Kefraya were waiting, one resident said he was not yet sure where he would live.
Madaya and Zabadani have been under the control of anti-government fighters but facing siege from forces loyal to the regime.
The convoy was carrying residents and pro-government fighters from the Shi'ite villages of al-Foua and Kefraya, which are besieged by rebels in nearby Idlib province, an insurgent stronghold.
We urge all parties involved in to guarantee the safety of people who are now seeking for safer places and call for prosecution of those responsible for this attack, he said.
It's the same with Madaya and Zabadani, as the army entered Madaya on Friday following the evacuation of the first batch of rebels and their families. An AFP correspondent, west of Aleppo speaking before the reports of an explosion, said coaches carrying government evacuees had not moved in 30 hours.
Afandar said people were not allowed to leave the buses for a while before they were let out. After the blast, evacuees from opposition areas pleaded for protection fearing revenge attacks.
An opposition representative, Ali Diab, told the pan-Arab Al-Arabiya TV that fewer armed men than agreed to were evacuated from the pro-government areas, violating the terms of the deal.
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