The incident, in Bronwnsville, comes on the heels of the deadly police shooting of a 16-year-old boy in East Flatbush two weeks ago that left the community reeling and led to several violent protests.
Police cars still stand guard at the entrance to Grafton Street, where the incident happened around 6:15 p.m. Thursday.
Authorities are still trying to determine exactly what led to the shooting.
The suspect has been identified as 20-year-old Shaquille Reid, who they say fired a Colt .45 semi-automatic handgun at undercover cops. The officers returned fire, striking Reid in the buttocks and the hand. The weapon was reportedly recovered at the scene.
The shooting happened as the officer and detective, both part of the Brooklyn South Narcotics Task Force, were working on an undercover buy-and-bust operation in street clothes and an unmarked car.
That's when officers say they saw Reid pull out the gun. They approached him, and that's when he allegedly fired at them.
Residents say the neighborhood is besieged by crime, and one woman said even the huge police response doesn't make her feel safer.
"This neighborhood, every weeks it's something," she said, preferring to remain anonymous. "Every week it's something around here...Right now, I don't even know [if I feel safe], to be honest."
The incident happened not that far from the East Flatbush neighborhood where police shot and killed 16-year-old Kimani Gray, a reputed gang member who allegedly pulled a gun on officers.
Reid is being treated for non-life threatening injuries at Brookdale Hospital. He is charged with criminal possession of a weapon and menacing.