About 149 pilots and first officers had already reported sick for Wednesday, Air Berlin chief Thomas Winkelmann said, according to an internal memo seen by dpa.
About 150 pilots called in sick today, Air Berlin said.
It seems like sickness is in the air since their cancelled flights aren't. Some short-haul flights at Lufthansa's budget airline Eurowings were also hit because it leases 33 planes with crews from Air Berlin.
The German government has provided the insolvent company with a credit facility of 150 million euros (179.8 million USA dollars) to ensure continuity of operations until a buyer is found.
Air Berlin filed for bankruptcy protection last month after its biggest shareholder, Etihad Airways, withdrew funding following years of losses. "A stable operation is mandatory for these negotiations to succeed".
As Air Berlin teeters on the brink of collapse, thousands of its passengers have had their travel plans wrecked by a "sick-out" involving flight crew. "That's the only way we can secure as many jobs as possible".
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An industry source said Air Berlin could lose 4 million to 5 million euros a day because of the cancellations.
Germany's giant services sector union Verdi on Tuesday expressed solidarity with the absent pilots and warned that more workers could call in sick.
Germany's transport minister is appealing to pilots at bankrupt Air Berlin to abandon an apparent wildcat strike that has caused two days of disruption.
"The fear and anger among Air Berlin staff is escalating because the future of whole families is at stake".
The airline has experienced financial difficulties for years, and it's only operating by a Government loan.