The shooting happened at New Jersey Avenue and Livonia Avenue just before 5 a.m. in a busy neighborhood with a school nearby.
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Police say the 40-year-old sergeant was on his way to work when he shot 21-year-old Thayvone Santana during an alleged holdup.
When police arrived, the sergeant told them Santana was a stranger and had tried to rob him.
But a family spokesman says in fact the two know each other, and had been fighting over a woman for weeks before the violent encounter at dawn.
"There are certain things that we saw in this investigation that we have questions that we want answered at this point, until we answer that we felt it was best to place him on modified duty," said NYPD Chief of Department Terence Monahan.
The sergeant said he believed Santana was armed, but it is not clear if he was.
WATCH: NYPD update on the incident
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Detectives have recovered video of the confrontation, which Eyewitness News has learned shows Santana with his hands in the air.
The sergeant says the man approached him, positioned his hand as if he had a gun, and said something to the effect of, "You're going to die tonight."
The sergeant fired his weapon twice, hitting him once in the chin.
The alleged would-be robber was taken to Brookdale University Hospital where he is expected to survive. No weapon was recovered at the scene.
The sergeant, assigned to the 109th Precinct in Queens, was not injured, but was being checked out for ringing in his ears.
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Authorities say the suspect was most recently arrested on a gun charge in Brooklyn. His prior arrests include robbery, gun possession and drug charges.
An undercover police informant told Eyewitness News that there is a problem with gangs and illegal guns flooding the neighborhood.
"It's basically a dead area, where drugs are coming, where weapons are coming," he said. "Because, I'm not saying the police are not doing enough, but they need to police it more."
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