The Al Qaeda-linked rebel groups on Saturday prevented the evacuated Shias from reaching their destination in Syria's Aleppo city, hindering a deal with the government, a source said.

Around 5,000 pro-government Shias evacuated the besieged towns of Kafraya and Foa on Friday and headed towards Aleppo under a deal between the government and rebels that should also see the evacuation of rebels and their families from rebel-held areas, Xinhua news agency reported.

The convoy of the Shias made a planned stop at the rebel-held town of Rashidien as around 2,300 rebels and their families left Madaya town towards Idlib province and also stopped at the government-controlled Ramouseh area in Aleppo.

Ramouseh and Rashidien are the places for the swap between both parties, but the rebels of the Front for Liberating the Levant, previously known as the Al Qaeda-linked Nusra Front, prevented the buses from Kafraya and Foa from proceeding towards Aleppo.

The government in return kept the rebels and their families from Madaya town from proceeding towards Idlib.

According to the source, the rebels had last minute demands and changes to the original deal.

He said the deal was brokered by Iran on the government side and Turkey and Qatar on behalf of the rebels.

The rebels' backers have apparently backed down on their pledges to see the abidance by the deal from the rebel side, he said.

Efforts were being made to see the deal through in the next hours, as there were other Shia batches from Zabadani town, he said.

"Around 500 rebels, mainly commanders from Zabadani near Madaya and 2,000 people from Kafraya and Foa are still in their places and were supposed to evacuate once the first batches arrive to their respective destinations," the source said.

The deal from Kafraya and Foa on one side and Madaya and Zabadani on the rebel side is considered the largest ever in Syria as the entire population of the Shia towns will leave.

Some of the Madaya people refused to leave with the rebels and their families and chose to remain in their area with some rebels who accepted a reconciliation with the government forces.

Now as Madaya is clear of the rebels, the Syrian Army entered the area after two years of laying siege to it.

In Zabadani, 500 rebel commanders are set to leave in the second batch.

This will largely contribute in expanding the security range around Damascus, particularly as Madaya and Zabadani are both close to the Lebanese borders and were conduits for the smuggling of weapons and radical fighters.

Still, opposition activists slammed the deal as another attempt for "demographic cleansing".

The deal's first step started on Wednesday with a detainee swap between the rebels and the pro-government fighters in Idlib.