The Conrail train went off the tracks just before 7 a.m. near Union Station on Green Lane in Union.
About 20 freight cars were impacted.
NJ Transit service between Cranford and Newark Penn Station was suspended as crews worked to clear the area.
No injuries were reported and there were no hazardous materials on the train.
Conrail workers removed the undamaged train cars but workers are still repairing the tracks.
Raritan Valley Line service will continue running on a modified schedule on Wednesday, with trains operating between High Bridge and Cranford.
Limited service will operate to and from High Bridge. Substitute bus service will operate from Cranford to Newark making stops at Roselle Park and Union Station.
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