Authorities say the train became disabled around 3:25 p.m. Friday due to an Amtrak overhead power problem.
A New Jersey Transit spokeswoman says the train finally reached Penn Station just before 6 p.m.
The loss of power caused delays of an hour or more on both Amtrak and New Jersey Transit.
Amtrak is assessing the extent of the damage.
A passenger from the disabled train became belligerent and sparked a stampede among passengers leaving the overcrowded station.
Police said reports that shots were fired at the station are not true.
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