Lufthansa's low-priced division Eurowings - which is wet-leasing Airbus A320-family jets from Air Berlin - has been affected.
"At the moment more than 110 flights have been canceled, with about 12,000 passengers affected", the spokeswoman said.
Air Berlin announced on September 11, that it would be ending Caribbean flights from the airline's hub is Dusseldorf, Germany on September 25.
The airline's chief executive, Thomas Winkelmann, accused pilots of "playing with fire", as the cancelled flights would cost the company several million euro, making it less attractive to potential buyers. He states: "We are in the middle of final talks with potential investors".
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Air Berlin continues to fly during the preliminary insolvency proceedings due to an EU-approved loan of EUR€150 million (USD$179 million) agreed at the beginning of September.
German flagship carrier Lufthansa - which already leases 38 of Air Berlin's 140 planes - could buy up to 70 aircraft with as many as 3,000 crew for Eurowings, German media had reported.
The Gulf-based company said last month the decline of Air Berlin was "extremely disappointing", especially as it had provided extensive support to the German carrier over the past six years, notably with a €250m (£227m) cash injection in April this year. "A stable operation is mandatory for these negotiations to succeed".
Pilot union Vereinigung Cockpit says it is "surprised" by the cancellations and stresses that it has not called on its members to call in sick. "This is the only way we can protect as many jobs as possible".