On its website, Air Berlin cited “operative reasons” for the cancellations on Tuesday, and asked passengers to call a helpline and refrain from travelling to the affected airports.
Because the carrier no longer offers compensation for cancelled flights, customer advice centres recommended that people affected by the strike book replacements at their own expense.
Berlin’s Tegel airport and Düsseldorf airport, Air Berlin’s hubs, were hit hard by the strike action, which also affects 42 planes run by Air Berlin on behalf of Eurowings and Austrian Airlines.
Spiegel Online said about 250 pilots called in sick on Tuesday morning. Air Berlin employs approximately 1,500 pilots.
Vereinigung Cockpit, a collective bargaining group for German pilots and flight engineers, has expressed concern that the airline is planning to offload its long-haul flights branch, which pays staff higher wages.
Air Berlin has already announced that it will cease to operate flights to the Caribbean and Boston from 25 September.
Air Berlin made a loss of €782m (£703m) in 2016. Last month, Etihad Airways, which owns almost 30% of Air Berlin, said the developments were “extremely disappointing”, but it could not keep injecting cash after investing an additional €250m in April.
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