The officer suffered minor injuries, while the other driver was uninjured, according to police.
The crash occurred at Route 110 and Broadway at 11:38 p.m.
Police said the officer had observed a motorist, headed north on Route 110, run a light - and turned on his emergency lights and siren to initiate a traffic stop. As the officer proceeded into the intersection, a westbound vehicle, whose driver, police said, had an obstructed view of the intersection, struck the rear quarter-panel of the police cruiser.
The driver was not injured. The officer suffered minor back injuries and was taken to Huntington Hospital, where he was treated and released. The driver of the car that police said ran the red light was not stopped and no summonses were issued.