The pedestrian was struck while crossing near the intersection of 10th Street and 40th Avenue in Astoria around 12:45 a.m. He was not in the crosswalk.
He was pronounced dead at the scene.
The NYPD says the police cruiser, which was responding to a report of a domestic dispute with a weapon in the Queensbridge Houses, had its lights and siren on.
The report turned out to be unfounded.
One eyewitness who didn't want to be identified told reporter Josh Einiger what she saw.
"His head was busted real bad," she said. "His legs was twisted. Everybody was saying, you know, that was it for him. He was still breathing a little. He was taking deep breaths, trying to hold on."
She added that the officers did nothing to try and help the man, just putting a sheet over his face.
"They was making everyone back up toward the sidewalk," she said. "They just left him lying in the street. They wasn't trying to help him or anything. It's sad. Real sad."
The two officers in the cruiser were assigned to PSA 9, a precinct that patrols city housing authority buildings.
The officers were taken to New York Hospital of Queens to be treated for trauma.
The crash is under investigation.