The warning strike, which started at 0500 GMT and is scheduled to end at 0830 GMT, was having a greater impact than a shorter two-hour strike on Feb. 12, mainly because the airport's fire department added its force to the protest.
"If the fire department is not working, we cannot do anything," said a spokesman for Lufthansa's Germanwings carrier.
Berlin has Germany's third largest air traffic volume after Frankfurt and Munich. About 21 million passengers fly through the capital city every year.
Public service sector union Verdi is pushing for an 8 percent pay rise for workers at the two airports, Tegel and Schoenefeld, which employ 1,500 people. Verdi said 300 workers took part in the strike.
Verdi said Berlin airports have offered a 1.3 percent pay rise for 2009. The airport has said it had made a 2.6-percent wage increase offer combined with a 1,250-euro ($1,593) one-off payment that would give an overall wage increase of 4.2 percent.
German flagship carrier Lufthansa cancelled around 12 domestic and European flights and expected additional delays.
Unit Germanwings was scheduled to operate three flights during the strike period. Peer Air Berlin had to cancel or delay 18 flights into and out of Berlin.