It happened in the Canarsie section around 9:45 p.m. Friday.
According to officials, officers were responding to shots fired in the area of East 80th Street and Flatlands Avenue.
Officers were already in an unmarked vehicle when they saw a man exiting a convenience store.
The man apparently spotted the officers and took off running. At least two officers chased the man on foot, while others pursued him in their cruiser.
Police say the man hid behind a tree, turned and pointed a gun at a police sergeant.
"The officers verbally identified themselves and gave the male numerous verbal commands to which he did not comply," Philip Rivera, NYPD chief of patrol, said in a news conference.
At least four officers fired their weapons at the man, striking him in the stomach.
The suspect was taken to nearby Brookdale Hospital.
Officers recovered two guns at the scene. One was a ghost gun, which was recovered inside the convenience store.
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