The mass "sick-out" comes ahead of a Friday deadline for potential investors to submit bids for Air Berlin assets.
"More than 30 flights" had to be scrapped today as some 150 pilots handed in sick notices for a second day, an Air Berlin spokeswoman said.
Duesseldorf and Berlin-Tegel airports were worst hit by the cancellations, she said, advising affected passengers "not to come to the airport".
Thousands of travellers were already left stranded on Tuesday when some 200 of Air Berlin's 1,500 pilots suddenly called in sick, forcing the cancellation of around 100 flights.
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Lufthansa's low-cost subsidiary Eurowings, which leases Air Berlin aircraft and crew, was also affected for a second day.
Air Berlin filed for insolvency in mid-August, after its main shareholder, Gulf carrier Etihad Airways, unexpectedly pulled the plug on its cash lifeline.
The airline has long struggled for survival, and booked losses amounting to 1.2 billion euros ($1.4 billion) over the past two years.
Germany's giant services sector union Verdi on Tuesday expressed solidarity with the absent pilots.
"All the conversations surrounding insolvent Air Berlin are always about its economic interests, never about the jobs of its more than 8,000 employees," said Verdi board member Christine Behle.
Air Berlin's insolvency has placed "a huge strain" on the airline's employees, "especially given the uncertainties surrounding the fate of jobs," he said.
"That's precisely why it's important to keep flight operations going as best as possible," he told the Bild newspaper.
German flagship carrier Lufthansa -- which already leases 38 of Air Berlin's 140 planes -- is seen as the favourite to take over the bulk of the stricken carrier's assets.
Other interested suitors cited in media reports include package holiday firm TUI, British low-cost carrier EasyJet and Thomas Cook subsidiary Condor, as well as Bavarian entrepreneur Hans Rudolf Woehrl.