An explosion hit a bus convoy carrying evacuees near the Syrian city of Aleppo.
The Britain-based Syrian Observatory for Human Rights monitoring group said government forces entered Madaya after the evacuation Friday.
The Syrian Observatory for Human Rights said the attack in Rashidin, west of Aleppo, targeted residents evacuated from the northern towns of Fuaa and Kafraya under a deal reached between the regime and rebels.
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.
According to the deal, more than 2,000 residents, activists and gunmen from areas besieged by government forces were also evacuated.
The predominantly Shiite towns of Foua and Kfraya have remained loyal to the Syrian government while surrounding Idlib province has come under hard-line Sunni rebel rule.
On Saturday, those from Madaya sat outside rows of coaches in a bus garage in government-held Aleppo, waiting to move onto Idlib, pictures sent by a pro-opposition activist showed.
A senior rebel leader said 20 fighters guarding the buses were killed along with dozens of passengers.
An AFP correspondent at a marshalling point in rebel-held territory where around 5,000 evacuees from two government-held towns were awaiting onward transport said the buses had yet to move 30 hours after the operation began.
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The residents of Madaya had an option to stay there, though Alison reports that "many say they'll leave to avoid mandatory service in the Syrian army".
Some 30,000 people are being relocated from two rebel-held towns and two under government control but, according to AFP news agency, up to 5,000 government evacuees and 2,200 from rebel towns are now stranded.
Dozens of buses carrying civilians from opposing side of the six-year civil left as planned on Friday but were held at depots overnight, parked up separated by a wall on the outskirts of Aleppo city.
A resident of Zabadani, Amer Burhan, said no evacuation had taken place.
In Syria's south, the opposition-held towns of Madaya and Zabadani had been surrounded by government and Lebanese Hezbollah forces.
Madaya and Al-Zadabani, both of which are located some 40 kilometers northwest of Damascus, are now encircled by regime forces, while Kefraya and Al-Fuaa - both in Syria's northwestern Idlib province - remain encircled by opposition forces.
"We are anxious about the reaction of the regime for what happened", he said.
They are also causing demographic changes because those who are displaced are usually Sunni Muslims, like most of the opposition. Assad is from the Alawite religious minority, often considered an offshoot of Shia Islam.