An enormous and complex logistical operation involving thousands of EU and other officials was launched to ship migrants and refugees from Greece back to Turkey under a controversial accord between Brussels and Ankara.

In the first wave of deportations on Monday, around 200 mostly economic migrants from Pakistan, Bangladesh and Afghanistan were sent back to Turkey aboard chartered Turkish ferries sailing from the Greek islands of Lesbos and Chios.

Under the hard-won deal with Ankara, the European Union accepted that for every refugee from war-ravaged Syria being returned to Turkey from Greek islands, another Syrian refugee would be resettled directly from Turkey to the EU.

While the operation ran smoothly on the first day, human rights groups feared for the future of asylum seekers.

Many worried that Greece was overwhelmed with potential asylum seekers, and that authorities did not have the resources to process their applications - meaning that some refugees would be deported without exercising their right to apply for refuge.

Deportations of refugees and migrants from Greece to Turkey begin calmly but human rights fears over future persist 

"There are many questions over the legality of this deal, largely because we have little information as to whether or not people have a fair chance of having their asylum claims assessed. This [deportation process] appears to have been fast-tracked," Brad Blitz, who researches migration in the southern Mediterranean at Middlesex University, told Al Jazeera.

"Some [migrants and refugees] did leave voluntarily. The first two boats [on Monday] contained principally Pakistani migrants. The third boat contained Afghans."

He added that migrants and refugees from South Asia were more likely to face return at the initial stage of the operation, as opposed to those fleeing war-ravaged countries such as Syrians.

"Everyone has the right to seek asylum," Blitz said. "People have the right to fair process. Their claims should be assessed. We know very little about how decisions are being made."

The governor of Turkey's Izmir province, Mustafa Toprak, said that three boats carrying 202 refugees had reached the shores of Dikili, adding that there were no Syrians on board.

READ MORE: UN urges leaders to accept more Syrian refugees

Later on Monday, 16 Syrian refugees landed in Germany on a flight from Turkey as part of the deal, which caps the number of those who will be allowed to enter Europe under the agreement at 72,000.

All "irregular migrants" arriving in Greece from Turkey since March 20 face being sent back across the Mediterranean under the deal.

"What happened on Monday morning was a message from Europe that the door for illegal migration is closed," said Al Jazeera's Zeina Khodr, reporting from Lesbos.

"They wanted to send this strong message because just yesterday 500 refugees landed on Greece's shore, just a day before the deal was to be implemented."

Gauri van Gulik, deputy Europe director at Amnesty International, said that she feared refugees fleeing war and persecution would eventually be forced to go to Turkey.

"We're deeply concerned this is the first of many mass returns to Turkey. We're mostly worried about the next groups - what's going to happen when Syrians and people who are clearly refugees are going to be put on these boats?"

'Common policy' needed

Two Turkish ferries on Lesbos, and another one on Chios, picked up the refugees who were escorted by police from the EU border agency Frontex.

Turkish Interior Minister Efkan Ala had said his country was ready to receive 500 refugees on Monday and Greek authorities had provided 400 names.

READ MORE: The dark side of the refugee deal

The European Union signed the deal with Turkey as it wrestled with the continent's worst refugee crisis since World War II, with more than one million people arriving last year.

About 4,000 refugees have been detained on Greek islands since the agreement came into effect.

"The long-term challenge is that it is absolutely clear that a common European policy is the only way Europe can address this [crisis]," said Peter Sutherland, the United Nations Special Representative of the Secretary General (SRSG) for International Migration.

"Refugees are entitled to asylum. There's very little sign that this principle is being accepted across Europe."

Source: Al Jazeera and agencies