At least 80 percent of rebel fighters have already pulled out of the battleground Syrian city of Homs and the rest will leave on Thursday, the provincial governor told AFP.

The negotiated withdrawal from the city centre where the rebels had held out under tight siege for nearly two years is the first in more than three years of conflict.

It leaves the rebels confined to a single district in the outskirts of a city that what was for long an iconic bastion of the uprising and Governor Talal Barazi said negotiations were well advanced for the rebels to leave that neighbourhood too in the coming weeks.

"Eighty percent of the rebels have left the city. The remaining 20 percent will leave on Thursday," Barazi told AFP.

"On Wednesday, 980 people left, the great majority rebels but some of them civilians, including women and children."

He said just 300 to 400 people now remained in the Old City where the rebels had held out for so long and they too would be bussed out on Thursday to the opposition-held town of Dar al-Kabira, 20 kilometres (13 miles) north of Homs.

The withdraw leaves the whole of the city in government hands except the Waer neighbourhood in the northwestern outskirts and Barazi said he expected a similar evacuation agreement to be reached there soon.

"In Waer things will be easier and in the coming weeks new deals will be announced to restore security," he said.

The government allowed the remaining rebels in Homs to pull out with some of their weapons in return for the release of dozens of prisoners and hostages held by opposition fighters and the delivery of relief supplies to two pro-government towns in the north which they have besieged.

It is not the first deal between the government and the rebels -- a number of ceasefires have been agreed in the outskirts of Damascus.

But it is the first time that rebel fighters have withdrawn from an area they controlled under an accord with the government.