According to German government figures, between January and September, a total of 222 planned deportations were classified to have "failed" due to pilot refusal.
The majority of the stopped flights came from the country's main airline Lufthansa and its subsidiary Eurowings.
Around 140 refusals occurred at Germany's largest airport, Frankfurt Airport.
Michael Lamberty, a spokesman for Lufthansa, said that pilots sometimes had to cancel flights due to security concerns. The decision not to carry a passenger was ultimately down to the pilot on a "case-by-case decision."
"The decision not to carry a passenger is ultimately made by the pilot on a case by case basis. If he or she had the impression that flight safety could be affected, he must refuse to transport the passenger," media outlets quoted the spokesman as saying.
"Should security personnel at the airports have some sort of information in advance which indicates that a situation could escalate during a deportation, they can decide ahead of time not to let the passengers board."
Pilots can face disciplinary measures if they refuse to fly on moral grounds.
In 2017 so far, Germany processed more asylum applications than all the other European Union countries combined, according to the German immigration office.
In recent months, dozens of Afghan have returned to the country after their asylum applications were rejected by the German government.
The men face an uncertain future in a country struggling with high unemployment, a weak economy and masses of refugees as well as hundreds of thousands of others uprooted by war.
The developments come as German Chancellor Angela Merkel has been battling to bring down the numbers of asylum seekers after the arrival of more than one million refugees -- mainly from Iraq, Syria and Afghanistan -- hoping to find refuge in 2015 and 2016.
While Germany granted safe haven to most people from Syria, Berlin has argued that it can safely repatriate people to the capital Kabul and other parts of Afghanistan, even as Taliban and Daesh Takfiri militants terrorize much of the country.