Fifty Afghans whose asylum requests had been rejected were to have boarded the aircraft for their home country late Wednesday, but "in fact, only 18 got on the flight," said interior ministry spokesman Tobias Plate.
But he sought to play down the issue, saying that "if one looks at other flights, the numbers are always below that of the planning figure".
"There are always a few who don't turn up because of different reasons - health reasons, successful applications for urgent rights protection of which there are three cases here.
"Others go into hiding or seek asylum in churches," he said, adding that the proportion of no-shows increase when the planned expulsions are known ahead of time.
"That's why the government has initiated several measures, including for example no longer announcing such flights in advance," added the spokesman.
This week's group were part of a third wave of repatriations from Germany to Afghanistan since December under a disputed Afghan-European Union deal aimed at curbing the influx of migrants.
Nearly 80 Afghans, all men, have so far been sent back after their asylum applications were rejected by the German government.
Chancellor Angela Merkel has been battling to bring down the numbers of asylum seekers after the arrival of more than one million migrants seeking refuge since the summer of 2015.
While Germany granted safe haven to most people from war-torn Syria, Berlin has argued that it can safely repatriate people to Kabul and other parts of Afghanistan, where German troops are part of NATO forces seeking to create stability.
But the government has faced opposition from several regional state governments against sending Afghan nationals back to an increasingly dangerous environment.