Another ferry left from the island of Chios and brought the total number of migrants transported to 202, according Frontex, the EU border agency.
It said 180 Frontex officers along with Greek officers were deployed to escort the migrants. Greek riot police squads also boarded the boats before they set sail, The Associated Press reported.
Human Rights Watch's Eva Cosse called Monday a "turning point" that could be a harbinger of a "gross violation of human rights."
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"There's no transparency for the procedures," she said from Lesbos, describing how officials have refused to grant international monitors access to the deportations. "We have real concerns that they are hiding things."
Protests surrounded the entire process. A banner reading "RepealTheDeal" was hung across from the harbor in Greece while protesters flew a "Wake Up Europe" banner just inside.
Under the deal, Turkey agreed to take back refugees and migrants that had made it to Europe from its shores. In exchange, the EU agreed to settle thousands of Syrians already in Turkey — one for each Syrian Turkey takes back from the Greek Islands.
Oxfam said Monday that starting to send migrants back to Turkey moved Europe "yet another step closer" to a policy of indifference.
“Instead of coming together to resolve the crisis, European countries have built fences and shifted a humanitarian crisis away from its door," said Oxfam's Sara Tesorieri in a statement. "People who have been forced to flee conflict, disaster and poverty are being treated in ways contrary to the spirit of international law.”
The ferries' arrival Monday in Turkey was mostly shrouded in secrecy, according to rights organizations and reporters on the scene.
Tarp put up on boat and surrounding area where media is waiting. Hard to observe much, & no access to registr tents pic.twitter.com/ZhtY5B33iv
Even as the first migrants were sent back, more were trying to make their way to Europe.
A few hours after the first boat of returnees set sail from Lesbos, Greek coast guard patrol vessels rescued at least two dinghies trying to reach the island, The Associated Press reported.
Melissa Fleming, spokeswoman for the U.N. refugee agency, said there were 58 people rescued.
"We are just going to try our chance. It is for our destiny. We are dead anyway," Firaz, a 31-year-old Syrian Kurd, told the AP.
Cassandra Vinograd is a Senior Writer and News Editor. Before joining NBC News, she worked as a London-based correspondent for The Associated Press and specialized in politics, foreign affairs and defense.
Vinograd previously worked as an editor for The Wall Street Journal in Brussels and London.
She has reported extensively from Afghanistan and on West Africa and the Middle East.