The incident happened at 130th Street and Sutter Avenue in South Ozone Park around 5:30 a.m. after authorities say the agent witnessed four men trying to break into his car.
The suspect was reportedly shot in the back and taken to Brookdale Hospital.
The federal agent, a member of the FBI, was not injured.
The other three people fled the scene in a vehicle, and police were searching for them.
The exact circumstances of the shooting are not known, and it's not clear how many shots were fired. Most neighbors say they didn't hear anything because their air conditioners were blasting overnight.
It is also not clear what happened to the suspect, but a trail of blood stretched at least 50 feet.
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