The disruption began around 0300 GMT and is expected to last for one day, leaving almost all passenger and cargo flights grounded.
A total of 204 flights were cancelled at Schoenefeld airport and 455 at Tegel, an FBB spokesman told AFP.
Berlin ground crews walked out twice in February as service workers' union Verdi piles on pressure in wage negotiations.
The union is fighting for higher salaries for workers registering passengers and loading baggage at airports around Germany, with around 2,000 of them based in the capital.