The accident happened at about 3:45 p.m. just west of Centre Avenue in East Rockaway.
A person inside the vehicle was removed conscious and alert, and taken to a local hospital.
The cause of the accident remains under investigation, but the MTA said it appears the person drove around the crossing gates, which were down, and drove onto the tracks.
Service was suspended in both directions between Lynbrook and Long Beach as emergency crews responded to the scene, but later resumed.
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