A few dozen police and immigration officials waited outside a small white tent on the quayside at Dikili as the returned migrants disembarked one by one, before being photographed and having their fingerprints taken behind security screening.
The returnees from Lesbos were mostly from Pakistan and some from Bangladesh and they had not applied for asylum, said Ewa Moncure, a spokeswoman for EU border agency Frontex.
Asked if Syrians would be returned, she said: "At some point, but I don't know when."
Turkish EU Affairs Minister Volkan Bozkir said there were no Syrians in the first group coming from Greece, but that when they did begin to arrive they would be sent to the southern city of Osmaniye, around 40 km (25 miles) from the Syrian border.
For non-Syrians, Turkey would apply to their home countries and send them back systematically, Bozkir said in an interview with Turkish broadcaster Haberturk.
Rights groups and some European politicians have challenged the legality of the deal, questioning whether Turkey has sufficient safeguards in place to defend refugees' rights and whether it can be considered safe for them.
Turkey insists it is meeting its international obligations. The EU was determined to get the programme under way on schedule despite such doubts because of strong political pressure in northern Europe to deter migrants from attempting the journey. There were small protests as the returns got underway.
On Lesbos, a small group of protesters chanted "Shame on you!" when the migrant boats set sail as the sun rose over the Aegean. Volunteer rescuers aboard a nearby boat hoisted a banner that read: "Ferries for safe passage, not for deportation."
Each migrant was accompanied on Lesbos by a plainclothes Frontex officer.
They had been transported in a nighttime operation from the island's holding centre to the port. Greek riot police squads also boarded the boats.
The United Nations High Commissioner for Refugees (UNHCR) and rights groups have said the deal between the European Union and Turkey lacks legal safeguards.
Amnesty International has called it "a historic blow to human rights", and was sending monitors to Lesbos and Chios on Monday.
More than 3,300 migrants and refugees are on Lesbos. About 2,600 people are held at the Moria centre, a sprawling complex of prefabricated containers, 600 more than its stated capacity. Of those, 2,000 have made asylum claims, UNHCR said.