At the regime-held Wafideen checkpoint, the delayed evacuation came as a huge disappointment for families who were hoping to reunite with relatives who they say were being held by the rebels. Turkey, with support from rebels, is running its own military operations against a USA -backed Kurdish party that controls territory along the frontier.
An opposition source said talks over the densely-populated town of Douma, the last rebel pocket of eastern Ghouta, had yet to be concluded, at odds with state media reports that the group holed up inside - Jaish al-Islam - had accepted a deal to leave.
The Syrian Observatory for Human Rights, a war monitor based in Britain, said negotiations were under way to revise the deal.
And, while Failaq a-Rahman maintains close ties with the rebel factions that rule the Syrian northwest, including the hardline Hay'at Tahrir a-Sham (HTS) coalition, Jaish al-Islam does not.
The deal struck between the Army of Islam and the Russian military marks the end of a weekslong push by the Syrian government to consolidate its control of the suburbs.
He said Jaish al-Islam has 10,000 fighters and "more than 4,000 of them categorically refuse to leave".
"A clear message was sent to the Free Syrian Army (FSA) groups in the area: either reconciliation and disarmament - handing weapons to the Syrian government as the Russians describe it - or departing eastern Qalamoun", the rebel spokesperson was quoted as saying.
Turkey, Russia and Iran also said that they were already committed to achieve a "lasting ceasefire" in Syria, in a joint statement issued following their meeting held in the Turkish capital of Ankara.
Opposition officials, however, denied the reports.
He described mass evacuations of civilians as "desperate measures in desperate times" adding that they had played their part in ending battles in urban areas in Syria.
In Syria, the mass evacuation of civilians is threatening to leave aid workers "overrun" and "acutely underfunded", as details emerge of the unparalleled destruction in urban areas like the former ISIL-held city of Raqqa, UN senior adviser Jan Egeland has said. It was here that rebels transported weaponry and ammunition across eastern Ghouta. At least 170,000 people, including civilians and rebel fighters, have also been evacuated out of the area.