Fighters from the Faylaq al-Rahman group left Douma on buses sent by the Syrian government to the rebel-held province of Idlib, SANA state news agency reported.
Fighters from the Jaish al-Islam group will leave Douma to north Syria, possibly to the city of Jarablus, controlled by Turkish-backed rebels, a Syrian opposition source close to talks held between the group and Russian Federation told Asharq Al-Awsat on Sunday.
The Saudi-backed group, which has deep roots in the region, has held firm in recent weeks as virtually all the other insurgents of eastern Ghouta have reached deals to relocate to the rebel-held north, leaving Douma as the only remaining rebel holdout.
A Syrian military source was quoted as saying that some of the fighters were rejecting the deal.
In the past 24 hours, an additional 1,100 Jaish al-Islam fighters and their families have left the town of Douma in Eastern Ghouta, Russia's defence ministry also said. The evacuation deal for the militants from Douma is still valid, SANA said.
It was not immediate possible to confirm the details of the deal and there was no comment from the Army of Islam.
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Syrian government forces are reportedly close to taking full control of the opposition stronghold of Eastern Ghouta near the capital, Damascus.
The Army of Islam did not agree to leave the town, said Iyad Abdelaziz, a member of Douma's current local council.
Rebel fighters had held Ghouta since 2012, and recapturing it will be seen as a victory for Syrian President Bashar Al Assad. Some 50,000 fled to opposition-held Idlib, which Egeland called "the biggest cluster of displacement camps in the world" with around 1.5 million people.
A journalist who was at the meeting, said that after the meeting the three leaders expressed their increase in hope for peaceful solution in the Syrian crisis in light of the latest achievements after their trilateral talks.
A rebel faction trapped by Syrian government forces outside the capital agreed to evacuate to northern Syria on Sunday as talks continued over lifting the siege against the town of Douma, where tens of thousands of civilians await relief.
Russian Federation is a key backer of Assad.
Syria's army has discovered a complex network of secret tunnels in eastern Ghouta, including subterranean hospitals and strategic corridors used by rebel fighters to move weaponry and ammunitions.