More than 130 refugees, mostly from Pakistan and Bangladesh, were deported at dawn from the remote Greek island of Lesbos to Dikili, a small port town in Turkey.
A third boat carrying 66 migrants left from nearby Chios Island arriving in Dikili shortly after.
They are the first moves to enforce a deal between Turkey and the European Union but he UN Refugee Agency (UNHCR) says there are not enough adequate safeguards in place to ensure their safety.
"This is an unprecedented era, the world has never seen such mass displacement before", said Boris Cheshirkov from UNHCR.
Speaking from Lesbos Mr Cheshirkov said all countries need to help, "that means increasing resettlement quotas whether in Europe, North Africa or New Zealand".
In exchange for political and economic benefits Turkey agreed last Month to take back all migrants and refugees who had not applied for asylum or who had their asylum applications rejected.
For each Syrian refugee Ankara accepts, the European Union will resettle another Syrian in Europe.
But since the deal was brokered on March 20, Mr Cheshirkov said standards had deteriorated for refugees.
The Moria detention centre 10 minutes drive from the Lesbos Port, and where today's deportees were taken from, has become a closed facility since the deal.
UNHCR and other aid organisations say they have been forced to withdraw support at the centre as it is illegal to detain children or asylum seekers while their claims are being processed - something they will not be seen to encourage.
"There are 2800 people in the centre far beyond the cap of 2000, there are people are sleeping in the open and there are food shortages", Mr Cheshirkov said.
Frontex, which manages European borders and is facilitating the deportations, says the first boats left the Greek island without any problems but it had not taken any risks deploying one guard for every refugee being deported.
There were small protests including boats in the port holding a big banner, and letting off a flare before being ordered to leave by the Coastguard.
Frontex's spokeswoman in Lesbos, Eva Moncure, would not say when the next deportations would go ahead."