The SUV was hit at a crossing at Route 111 in Central Islip around 4:30 a.m. Monday.
It was not immediately clear whether the crossing gates were down, or whether the vehicle became disabled while on the tracks.
Fire damage was visible on the outside of at least one train car. However, the railroad said 31 passengers were safely evacuated moments after the crash.
The accident caused the suspension of all service on the Ronkonkoma branch between Farmingdale and Ronkonkoma.
By 10 a.m., the LIRR said the train had been removed from the tracks but that crews were still on the scene assessing the damage and making repairs.
Westbound service from Farmingdale is operating hourly until those repairs are finished and buses are operating in both directions between Ronkonkoma and Farmingdale.
For more information, visit www.mta.info/lirr.
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