PATH trains in and out of Hoboken were subject to delays of up to a half-hour as of just before 5 p.m.
Limited service resumed on the Northeast Corridor and North Jersey Coast lines with delays.
Tickets were cross-honored on PATH trains, as well as on buses, private carriers and New York Waterway ferries.
The "slow speed derailment" of the 3926 Northeast Corridor train occurred at about 9 a.m. in tunnel 9 of New York Penn Station, NJ Transit said.
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