Bankrupt Air Berlin said it was forced to cancel dozens of flights on Tuesday, after "an exceptionally high number" of pilots called in sick.
"We regret the inconvenience for our passengers," said the airline on its website.
Both domestic and international flights were affected, including links between Berlin and Los Angeles or Dubai.
Lufthansa's low-cost subsidiary Eurowings, which is renting aircraft as well as pilot and crew from Air Berlin, has also been forced to cancel some flights.
Air Berlin filed for insolvency in mid-August, after its main shareholder Gulf carrier Etihad pulled the plug on its cash lifeline.
The airline had for years struggled for survival, and booked losses amounting to 1.2 billion euros ($1.4 billion) over the past two years.
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.
The insolvent group is now hoping to complete its sale this month, with a Friday deadline for potential bidders to present their offers.
Lufthansa -- which already leases 38 of Air Berlin's 140 planes -- could buy up to 70 aircraft with as many as 3,000 crew for Eurowings, German media had reported.
Other interested airlines cited in media reports include package holiday firm TUI, British low-cost carrier EasyJet and Thomas Cook subsidiary Condor.
