An investigation determined the damage to the car -- a shattered windshield -- was "not consistent with shots fired," Suffolk County police said.
The incident occurred shortly after 9 a.m., police said.
Police said the driver, whose name was not released, called 911 to report his windshield had been damaged, possibly by gunfire, as he drove along Montauk Highway west of Station Road.
Police immediately notified the district, which placed Bellport High School and other schools on lockdown status.
The lockdown situation was lifted "almost immediately," police said, after it was determined the incident did not involve gunfire.
It was not immediately clear how the car was damaged.