The first Syrians arrived in Germany from Istanbul on Monday under a controversial EU-Turkey migrant pact, an official from the German federal refugee office told AFP.

The 32 asylum seekers flew into the northern city of Hanover on two separate flights and were to be taken to a shelter about 140 kilometres (90 miles) away.

The representative from the Federal Office for Migration and Refugees, Corinna Wicher, asked reporters to respect the privacy of the asylum seekers, who were members of six families. An AFP reporter saw 10 children and an adolescent in a wheelchair among the two groups.  

"This is all very new, very difficult," Wicher said. "They have been travelling for a very long time."

One protester also arrived to meet the group, holding a banner reading: "Please keep fleeing, refugees not welcome."

Wicher said the new arrivals would spend two weeks at the temporary shelter in the town of Friedland for orientation, including lessons in basic German and logistical practicalities, before being placed in housing around the state of Lower Saxony.

Under the scheme agreed with Turkey last month, one Syrian refugee will be settled in Europe legally in return for every Syrian migrant taken back by Turkey from EU member Greece, which has faced the largest influx in recent months.  

Early Monday, Greece sent back a first wave of migrants to Turkey under the deal that has run into strong criticism from rights groups.

Refugee advocates question whether the agreement is legal and ethical, fearing individuals will be denied the right to claim asylum. 

 'Shelters only half full'

 Germany last year let in a record 1.1 million migrants and refugees but Chancellor Angela Merkel has come under intense pressure to stem the flow.

Merkel, who spearheaded the deal with Ankara, spoke by telephone with Turkish Prime Minister Ahmet Davutoglu early Monday to discuss the start of returns and "agreed that the pact must be implemented successfully", her spokesman Steffen Seibert said. 

Berlin has agreed to accept 1,600 people out of a total of just over 22,500 under the current programme and expects other EU member states including France, Finland and the Netherlands to begin taking in refugees under the pact early this week, an interior ministry spokesman said. 

Germany has already seen a sharp drop in arrivals in recent weeks after Balkan countries closed their borders to migrants and refugees. 

The daily Bild reported Monday that more than half of the places available at reception centres, generally the first port of call for new asylum seekers, were now unfilled after months of overcrowding.

Among more than 348,000 places in shelters across the country, only about 157,000 are currently occupied, the newspaper reported after polling officials in Germany's 16 federal states.