The incident was reported on Beach Channel Drive and Dix Avenue just before 6 p.m.
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Police say officers drove into the middle of a confrontation between two men.
One of the men ran to the police car for help when the other man opened fire in that direction.
The cops jumped out of their car and returned fire.
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The gunman ran away and was last seen wearing all black clothing.
Tensions in the city led many to initially believe the officers were targeted, but that does not appear to be the case, according to police.
However, the NYPD said the officers were still confronted with a life-threatening situation, but fortunately they are only being treated for minor injuries.
In the tweet, police say it was the second time in a week a police cruiser was struck by bullets.
That refers to a shooting on Sunday, May 31, when a 21-year-old gunman allegedly opened fire at two officers sitting in a marked patrol car in front of a home in nearby Arverne, about two miles away from Wednesday's gunfire shootout.
The alleged shooter, Kane Motta, was arrested on attempted murder charges in what Queens District Attorney Melinda Katz called "a targeted attack on our law enforcement as they watched over a neighborhood on a quiet night in Queens."
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