Amtrak owns and operates the station. It says Northeast Corridor "customers may experience delays of 45 minutes in and out of the station."
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Officials say the train was carrying about 180 passengers and crew when it derailed Thursday night.
No injuries have been reported. Passengers were being transferred to another train to take them into the station.
Train service is suspended in and out of Penn Station.
NJ Transit says it's working with Amtrak to determine the cause of the slow-speed derailment.
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The busy Northeast Corridor area around Penn Station has been beset by problems recently. Two previous derailments, a power failure and signal problems have pushed Amtrak to begin replacing aging tracks and equipment and have caused numerous delays.
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