Syrian state TV broadcast pictures of buses leaving the rebel enclave and entering a government-controlled area.
A UN official also told Reuters news agency that the evacuation had resumed.
Activists said 60 buses were stuck in the rebel enclave overnight, forcing 3,000 people to wait in freezing weather with little to eat or drink.
Reasons for the hold-up were not clear. But state media blamed rebels in neighbouring Idlib province, accusing them of preventing the simultaneous evacuation of two pro-government Shia towns there.
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