"This morning, 27 people were returned to Afghanistan," the interior ministry announced on Twitter.
They include 17 who have been convicted of crimes, two who are deemed "dangerous individuals" and eight who have "stubbornly refused to give their real identities," it said.
The men left Germany late yesterday from Frankfurt airport, where around 600 people had gathered to demonstrate against the expulsions.
Despite the criticism, German Interior Minister Thomas de Maiziere vowed to press on with sending back "dangerous individuals, criminals and those who refuse to give their real identities".
Also Read
With public unease mounting over the new arrivals, Berlin struck deals, including with Turkey, to dissuade would-be migrants from trying to reach Germany.
Last year, Germany signed a deal with Kabul to repatriate Afghans who had failed to obtain asylum, and began expelling people in December 2016.
The government maintains that certain areas of Afghanistan are "safe" for repatriations, though it suspended deportations for a few months after a truck bomb ripped through the diplomatic district in Kabul in May, killing an Afghan guard at the German embassy and wounding two employees.
Around 200 students staged a sit-in in May at a vocational school in Nuremberg and clashed with police who came to detain for deportation a 20-year-old Afghan student who had been in the country for over four years.
In the first nine months of the year, 222 expulsion bids had to be scrapped because pilots refused to fly the planes, German news agency DPA reported.
Eighty-five of the 222 aborted flights were operated by national carrier Lufthansa or its subsidiary Eurowings.
Disclaimer: No Business Standard Journalist was involved in creation of this content