The vehicles burned on the second and third floors of the parking garage in Marine Park. Officials say there were as many as 120 cars being stored in the structure by a local car dealer.
Investigators are looking to talk to a person seen on surveillance video leaving the Kings Plaza shopping center parking lot before Monday morning's fire.
Eighteen firefighters and three civilians were being treated for smoke inhalation.
"None of these 21 injuries is life-threatening or critical, everyone is stable," the FDNY said. "Our members have various levels of smoke inhalation, heat exhaustion, working under those conditions. Smoke and heat, wearing what they wear, one can only imagine what they are going through."
Kings Plaza is currently closed due to the fire and smoke conditions in and around the mall.
People are asked to avoid the area during the FDNY response that drew 250-300 firefighters.
WATCH: NYC Fire Commissioner Daniel Nigro briefs reporters on the fire
"We are not sure yet how many of them burned, but many of these cars were involved in this fire, creating, if you were here earlier, a huge amount of black smoke, a very large amount of fire, confronting our people," the FDNY said.
WATCH raw video from the fire scene
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