The first three boats full of rejected refugees have arrived in Turkey as part of the EU migrant transfer deal, on what rights campaigners described as a "day of shame" for Europe.

At around the same time, a plane carrying the first 16 Syrian refugees sent directly to Germany under the terms of the deal landed in the central city of Hannover.

Frontex, the EU border protection agency, said the process taking around 200 mostly Pakistani and Bangladeshi nationals had gone smoothly.

But there was criticism over the lack of transparency surrounding the exchange, as well as the fact police appeared keen to get the jump on reporters, beginning moving the refugees some hours before scheduled.

Gerry Simpson, a senior refugee advocate with Human Rights Watch, called Monday an "historic day of shame" as the "dirty" migrant deal was implemented.

He told The Independent there was a "tremendous amount of uncertainty" about whether those being deported had been allowed access to fair asylum procedures.

Mr Simpson said: "Like a thief in the night, the EU kicked off its shameful refugee dumping deal under cover of dawn.

"Turkey has no asylum procedures in place, so whether these people are from Bangladesh, Pakistan or any other nation it can’t be said they have access to fair protection there," he said.

"We have a number of concerns right now, but number one is the concern that the EU is breaching European law by returning people who need protection to an unsafe country."

The failed asylum-seekers were expected to be returned by Turkey to their country of origin - sparking renewed concerns as to what will happen to refugees arriving from war zones.

Refugee crisis - in pictures Show all 27 1 /27 Refugee crisis - in pictures Refugee crisis - in pictures A child looks through the fence at the Moria detention camp for migrants and refugees at the island of Lesbos on May 24, 2016. AFP/Getty Images Refugee crisis - in pictures Ahmad Zarour, 32, from Syria, reacts after his rescue by MOAS (Migrant Offshore Aid Station) while attempting to reach the Greek island of Agathonisi, Dodecanese, southeastern Agean Sea Refugee crisis - in pictures Syrian migrants holding life vests gather onto a pebble beach in the Yesil liman district of Canakkale, northwestern Turkey, after being stopped by Turkish police in their attempt to reach the Greek island of Lesbos on 29 January 2016. Getty Images Refugee crisis - in pictures Refugees flash the 'V for victory' sign during a demonstration as they block the Greek-Macedonian border Refugee crisis - in pictures Migrants have been braving sub zero temperatures as they cross the border from Macedonia into Serbia. Refugee crisis - in pictures A sinking boat is seen behind a Turkish gendarme off the coast of Canakkale's Bademli district on January 30, 2016. At least 33 migrants drowned on January 30 when their boat sank in the Aegean Sea while trying to cross from Turkey to Greece. Getty Images Refugee crisis - in pictures A general view of a shelter for migrants inside a hangar of the former Tempelhof airport in Berlin, Germany Refugee crisis - in pictures Refugees protest behind a fence against restrictions limiting passage at the Greek-Macedonian border, near Gevgelija. Since last week, Macedonia has restricted passage to northern Europe to only Syrians, Iraqis and Afghans who are considered war refugees. All other nationalities are deemed economic migrants and told to turn back. Macedonia has finished building a fence on its frontier with Greece becoming the latest country in Europe to build a border barrier aimed at checking the flow of refugees Refugee crisis - in pictures A father and his child wait after being caught by Turkish gendarme on 27 January 2016 at Canakkale's Kucukkuyu district Refugee crisis - in pictures Migrants make hand signals as they arrive into the southern Spanish port of Malaga on 27 January, 2016 after an inflatable boat carrying 55 Africans, seven of them women and six chidren, was rescued by the Spanish coast guard off the Spanish coast. Refugee crisis - in pictures A refugee holds two children as dozens arrive on an overcrowded boat on the Greek island of Lesbos Refugee crisis - in pictures A child, covered by emergency blankets, reacts as she arrives, with other refugees and migrants, on the Greek island of Lesbos, At least five migrants including three children, died after four boats sank between Turkey and Greece, as rescue workers searched the sea for dozens more, the Greek coastguard said Refugee crisis - in pictures Migrants wait under outside the Moria registration camp on the Lesbos. Over 400,000 people have landed on Greek islands from neighbouring Turkey since the beginning of the year Refugee crisis - in pictures The bodies of Christian refugees are buried separately from Muslim refugees at the Agios Panteleimonas cemetery in Mytilene, Lesbos Refugee crisis - in pictures Macedonian police officers control a crowd of refugees as they prepare to enter a camp after crossing the Greek border into Macedonia near Gevgelija Getty Images Refugee crisis - in pictures A refugee tries to force the entry to a camp as Macedonian police officers control a crowd after crossing the Greek border into Macedonia near Gevgelija Getty Images Refugee crisis - in pictures Refugees are seen aboard a Turkish fishing boat as they arrive on the Greek island of Lesbos after crossing a part of the Aegean Sea from the Turkish coast to Lesbos Reuters Refugee crisis - in pictures An elderly woman sings a lullaby to baby on a beach after arriving with other refugees on the Greek island of Lesbos after crossing the Aegean sea from Turkey Getty Images Refugee crisis - in pictures A man collapses as refugees make land from an overloaded rubber dinghy after crossing the Aegean see from Turkey, at the island of Lesbos EPA Refugee crisis - in pictures A girl reacts as refugees arrive by boat on the Greek island of Lesbos after crossing the Aegean sea from Turkey Getty Images Refugee crisis - in pictures Refugees make a show of hands as they queue after crossing the Greek border into Macedonia near Gevgelija Getty Images Refugee crisis - in pictures People help a wheelchair user board a train with others, heading towards Serbia, at the transit camp for refugees near the southern Macedonian town of Gevgelija AP Refugee crisis - in pictures Refugees board a train, after crossing the Greek-Macedonian border, near Gevgelija. Macedonia is a key transit country in the Balkans migration route into the EU, with thousands of asylum seekers - many of them from Syria, Afghanistan, Iraq and Somalia - entering the country every day Getty Images Refugee crisis - in pictures An aerial picture shows the "New Jungle" refugee camp where some 3,500 people live while they attempt to enter Britain, near the port of Calais, northern France Getty Images Refugee crisis - in pictures A Syrian girl reacts as she helped by a volunteer upon her arrival from Turkey on the Greek island of Lesbos, after having crossed the Aegean Sea EPA Refugee crisis - in pictures Refugees arrive by boat on the Greek island of Lesbos after crossing the Aegean sea from Turkey Getty Images Refugee crisis - in pictures Beds ready for use for migrants and refugees are prepared at a processing center on January 27, 2016 in Passau, Germany. The flow of migrants arriving in Passau has dropped to between 500 and 1,000 per day, down significantly from last November, when in the same region up to 6,000 migrants were arriving daily.

The first vessel, the Nazli Jale, reached the port of Dikili accompanied by the Turkish coast guard.

The Lesvos and Erturk vessels arrived shortly after, bringing a total of 202 migrants from the Greek islands of Lesbos and Chios.

A Turkish government official, speaking anonymously, said there were "very few Syrians" among the passengers. The Associated Press reported migrants were loaded onto buses, addind there was no immediate word from authorities as to where they would be taken.

Just a few hours earlier there were clashes between police and local residents on Chios, after a protest was staged against the planned deportations there.

About 4,000 migrants and refugees have been detained on Greek islands since the migrant transfer agreement came into effect on 20 March.

Mr Simpson said conditions on the Greek islands themselves were another cause for concern.

"Refugees are faced with substandard humanitarian conditions, and have little access to proper food, sanitation or shelter," he said. "People are sleeping under open skies in modern Europe in 2016."

Migrants are deported to Turkey from the port of Mytilene on April 4, 201 (AFP/Getty Images)

No Syrians were present in the first group of migrants coming to Turkey from Greece on Monday, Turkish EU Affairs Minister Volkan Bozkir said, adding that any who do arrive in future will be sent to the southern Turkish city of Osmaniye, not back to Syria itself.

Syrians being sent directly to Europe as part of the exchange deal would be given safe passage to Germany, from where some will be moved on to other countries, he said.

Speaking on Monday afternoon, a spokeswoman for the UNHCR defended the deal, and said the returns so far had followed "normal policy".

Melissa Fleming said UNHCR workers had spoken to some of those being deported, and found they "did not express their intention to seek asylum".

Ms Fleming said the EU-Turkey deal is expected to carefully screen people who fear for their lives or "have a well-founded fear of persecution" if they are sent home or to another country.