The 16 asylum seekers flew into the northern city of Hanover and were to be taken to a shelter about 140 kilometres (90 miles) away. A second group of Syrians was to arrive in Hanover in the early afternoon, the official told AFP.
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 three families. An AFP reporter saw five children among them.
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 the EU 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.
Refugee advocates question whether the agreement is legal and ethical, fearing individuals will be denied the right to claim asylum.
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 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.
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.
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