"He's one lucky man," Kelly said while visiting Bellevue Hospital where Officer Kevin Brennan, 29, was taken after being shot, The New York Post reported.
The shooting occurred Tuesday night after Brennan and two plainclothes officers responded to a report of shots fired at a Brooklyn housing project.
Just as police pulled up to the Bushwick Houses, three men were seen running out of a building.
Police said Luis "Baby" Ortiz, 21, fired at Brennan after Brennan followed Ortiz into the building lobby.
Charges against Ortiz were pending early Wednesday.
The bullet that doctors removed from Brennan's skull was held up by Commissioner Kelly at a news conference, The New York Times reported.
Brennan is expected to make a full recovery, Mayor Michael Bloomberg said.
He was reported in critical but stable condition.