"Air Berlin is now seeing an exceptional high number of sickness reports of their pilots".
Meanwhile, German Transport Minister Alexander Dobrindt urged the pilots to end their "risky manoeuvre" and return to work for the sake of Air Berlin's roughly 8,000 employees.
"Passengers holding tickets for cancelled flights will be offered other travel options", the website states.
Lufthansa (Xetra: LHAB.DE - news) 's low-priced subsidiary Eurowings, which is renting aircraft as well as pilot and crew from Air Berlin, said it had also been forced to cancel some flights.
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. "That is crucial in order to bring talks with investors to a successful conclusion", Chief Operations Officer Oliver Iffert said in an internal memo.
Air Berlin, Germany's second-largest airline, filed for bankruptcy protection last month after shareholder Etihad Airways withdrew funding following years of losses.
"We are in the middle of final negotiations with potential investors".
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A deadline to submit bids to acquire Air Berlin or parts of it has been set for 15 September.
They announced the cancellation of more than 100 flights on Tuesday.
An empty Air Berlin counter at Tegel airport in Berlin.
The airline has experienced financial difficulties for years, and it's only operating by a Government loan.
Germany's giant services sector union Verdi on Tuesday expressed solidarity with the absent pilots.
"The fear and anger among Air Berlin staff is escalating because the future of whole families are at stake".