The move has also hit Lufthansa subsidiary Eurowings, which said it had been told by Air Berlin at short notice some of the flights the latter carrier runs for it could not be staffed.
After losing £2m per day in 2016, and seeing its financial life-support cut off when Etihad abandoned its investment in the company in April, Air Berlin is in liquidation.
"Besides, long-haul flights are not affected as Air Berlin is not operating any Airbus A330 on behalf of Eurowings".
"We are now conducting final talks with potential investors".
Air Berlin chief executive Thomas Winkelmann suggests that pilots who have absented themselves are "playing with fire".
Flights from Düsseldorf to Curacao, Cancun, Havana, Varadero, Punta Cana and Puerto Plata will end on September 25, Air Berlin said. Stable operations are a prerequisite for the success of these negotiations. "If the situation does not change quickly, we will have to terminate operations and, thus, any restructuring efforts", he warns.
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"That's the only way we can secure as many jobs as possible", he added.
However, union Vereinigung Cockpit said in a separate statement it was surprised by the absences and that it had not called on its members to call in sick. Verdi is likewise urging staff members to go to work "in order not to jeopardise jobs", but notes: "It can not be ruled out that this will occur with other employees too".
The airline filed for insolvency last month.
The German government has argued that competition rules prevent any single airline taking over Air Berlin, the country's second-largest carrier after Lufthansa.
Air Berlin said once it had received the offers from potential investors on Friday, it hoped to reach a decision by September 21.