Spokesman Dan Stessel says service was restored just before 5 a.m. Tuesday, nearly 17 hours after a derailment kept trains from using nine tracks.
Two cars of a Midtown Direct train carrying 300 people went off the tracks at 10:50 a.m. Monday. No one was injured.
Commuters faced crowded conditions in and out of New York on Monday night.
PATH trains and NJ Transit buses honored NJ Transit passes.
New Jersey Transit said all customers on the derailed train were safely detrained and walked to the station where they were re-accommodated accordingly.
Both cars of the derailed train were rerailed and track repairs followed.
It took some time to get a crane to the scene to rerail the train cars. The first one was rerailed at around 3 p.m. Monday, and the second one at 7 p.m.
The derailment caused such a big mess because of where it happened. The train blocked access by NJT, LIRR and Amtrak to half of the tracks at Penn Station. Tracks 1-10 were not accessible, so all three had to use tracks 11-21.
That forced some trains to be combined during the evening commute.
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