Berlin Airport, which operates Tegel and Schoenefeld, said 455 flights had been cancelled at Tegel and 204 at Schoenefeld as of 0615 GMT. The strike is due to run for 25 hours from 0400 local time (0300 GMT) on Friday.
Carriers including Air Berlin, Lufthansa, easyJet and Ryanair serve the two airports.
The industrial action comes as many trade visitors try to make their way home from the world's biggest tourism trade fair, the ITB, which ends in Berlin on March 12.
"We are ready for talks at any time, of course also over the weekend, and open for a new offer," said Enrico Ruemker, strike leader at trade union Verdi.
The airport operator advised passengers to check their flight status with airlines before setting off for the airport.
Reported by Georgina Prodhan; Edited by Nick Macfie
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