About 60 firefighters raced to the station, near Broadway, about 10:50 a.m., an FDNY spokeswoman said.
The initial call was for a smoke condition in the station, fire said.
Responders found that the substance was not smoke, but freon that leaked from a subway car's air conditioning unit, an MTA spokeswoman said.
Trains along the 1, 2, and 3 lines were temporarily disrupted until the smoke condition was brought under control about 11:20 a.m., the spokeswoman said. Trains were running again as usual by 11:30, officials said.
No injuries were reported.