Insolvent Air Berlin said it is cancelling around 70 flights on Tuesday after pilots called in sick in unusually high numbers.
Departures information on its website showed flights cancelled from a range of German airports including Berlin Tegel, Duesseldorf, Hamburg and Cologne.
TUIfly was also forced to cancel flights last year after many pilots called in sick, with their union saying staff were concerned that merger talks, since failed, could lead to job and pay cuts.
Representatives from pilots' union Vereinigung Cockpit were not immediately available for comment.
Air Berlin, Germany's second-largest airline, was forced to file for bankruptcy protection last month after shareholder Etihad Airways withdrew funding following years of losses.
Bidders are lining up to buy the airline's assets, with Lufthansa seen in pole position to acquire large parts of its rival.
Bidders have until Sept. 15 to submit binding offers, with a decision possible as early as Sept. 21, three days before a German national election.