Officer Brian Mulkeen, 33, was the second New York police officer shot dead by colleagues in the line of duty this year.
"This is a tragic case of friendly fire but, make no mistake, we lost the life of a courageous public servant solely due to a violent criminal who put the lives of the police and all the people we serve in jeopardy," New York Police Department Commissioner James O'Neill said.
The incident occurred after Mulkeen and two other officers got out of their vehicle to question the suspect at around 12.30 a.m. on Sunday.
The 27-year-old suspect fled, leading to a chase on foot.
A violent struggle broke out on the ground as Mulkeen and his partners attempted to apprehend the man, police said.
Video from a body camera recorded Mulkeen saying: "He's reaching for it, he's reaching for it." Shots were then fired and Mulkeen was struck twice, police said.
O'Neill said Mulkeen's partners fired 10 rounds at the suspect and Mulkeen fired five.
Mulkeen and the suspect were rushed to hospital, where they were both pronounced dead.
Police said they recovered a firearm from the scene that was not fired during the incident and was believed to have belonged to the suspect.
The suspect, who police did not identify, was on probation until 2022 for a narcotics-related arrest last year and had several prior arrests, including a burglary conviction, police said.
Mulkeen, who served more than six years with the NYPD, was the 37th law enforcement officer killed by gunfire in the line of duty in 2019, according to the Officer Down Memorial Page, a website that records police deaths.His death follows the friendly fire shooting of an NYPD detective in February as police responded to a reported robbery at a mobile phone store in Queens.