Police said the officer, whose identity was not released, was airlifted to Stony Brook University Hospital, where he was treated and released. The officer had to be extricated from his patrol unit, police said.
The other driver, a woman, was taken to Brookhaven Memorial Hospital with minor leg injuries, police said.
No one was charged.
The incident occurred at 10:04 p.m. on William Floyd Parkway as the officer responded to a 911 call reporting a robbery at a Dunkin' Donuts, police said. The cruiser, which police said had its emergency lights and siren operating at the time, was southbound on William Floyd when it was T-boned on the driver's side door at Victory Avenue.
Police said the three robbery suspects, one of them armed, were able to escape the store as a result of the accident.
No one was injured in the robbery, police said, but police are still searching for the trio.
The accident remains under investigation, police said.