Fire and Emergency were alerted by an automatic alarm at 11.05pm, and arrived on scene by 11.06pm with 15 fire engines attending the blaze.
Emergency crews came from around the region including Avondale, North Shore and Onehunga.
Malthus said the building was evacuated with no operable police cells in the station.
At one stage smoke could be seen billowing from the building.
A Fire and Emergency spokesperson said the fire was "significantly scaled back" by 2am and contained to the office area.
Fire response continued to monitor throughout the night, with one fire engine still on site this morning.
One firefighter sustained a minor injury after pulling a calf muscle. They were taken to hospital as a precaution and released shortly after.
The main station is unaffected and continuing policing business as normal.
The area where the fire started was previously a gym but is now an office area.