"The migrants are busy getting off the boat for identity and health checks," the official told AFP on condition of anonymity.
"The Greek side has informed us that there will be three more boats today."
The migrants will be taken by bus to reception centres in Kirklareli on the Bulgarian border, from where they are expected to eventually be deported back to their home country.
Late Thursday, Turkey's parliament approved a deal signed in 2010 allowing for the repatriation of Pakistani migrants, local media reported.
After getting off the ground, the deal quickly ran into trouble as migrants on the Greek islands launched a flurry of requests for asylum which legally prevents them from being deported.
This led to several days of delays between deportations.
The Greek government said those expelled had not requested asylum.
Turkey has promised to take back all irregular migrants landing on the Greek islands since March 20 -- a figure which currently stands at about 6,000 -- while Europe has agreed to resettle one Syrian refugee directly from camps in Turkey for each Syrian deported.
Turkey is also to receive six billion euros (USD 6.8 billion) in financial aid up to the end of 2018 for the 2.7 million Syrian refugees it is hosting.
While questions remain over how successful the deportations will be in the long-term in discouraging migrants from making the treacherous journey to Europe, the numbers arriving in the EU have fallen drastically in recent weeks.
This is largely due to an increased clampdown by Turkey on people smugglers and a greater effort in stopping migrants from crossing land and sea borders into Europe.
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