The beleaguered airline says it is "currently seeing an exceptional high number of sickness reports of their pilots", which has led to dozens of cancellations. Air Berlin employs approximately 1,500 pilots. At least 32 flights have to be canceled so far on Wednesday, mainly at Berlin-Tegel and Dusseldorf airports.
Frank Kebekus, the company's chief representative, said the events "seriously endanger the entire insolvency proceedings under self-administration" and that if the situation did not change quickly, "we will have to cease operations and thus any restructuring efforts".
After losing the lifeline of regular cash infusions from Gulf carrier Etihad in June, Air Berlin filed for insolvency on August 15. "A stable operation is mandatory for these negotiations to succeed". "That is the only way to secure as many jobs as possible", Mr Winkelmann said.
Other airlines, Ryanair included, are already waiting on the outcome of the conflict in an attempt to acquire a portion of Air Berlin's most profitable routes.
Lufthansa's low-priced subsidiary Eurowings, which leases Air Berlin aircraft and crew, was also affected for a second day.
Germany's giant services sector union Verdi expressed solidarity with the absent pilots and warned that more workers could call in sick.
Air Berlin is Germany's second largest airline and employs over 8,000 staff.
The airline Air Berlin has cancelled around 70 flights, including some at Zurich Airport, because of a pilot protest over the airline's uncertain future.
In order not to leave travellers stranded during the busy summer season, the German government agreed to provide a bridging loan of 150 million euros to keep the airline flying for three months.