A disabled Amtrak train was causing delays in and out of Penn Station in the middle of the Monday morning rush hour, the agency said.
The train got stuck in the north tube of the tunnels under the Hudson River at about 8:20 a.m., spokesman Jason Abrams said.
It was removed, and there were no injuries to the 163 passengers or to the crew members, Abrams said at about 9:15 a.m.
NJ Transit, which also uses the tunnels, and Amtrak service was impacted for several hours after the train got stuck.
There were about 30-minute delays on Amtrak and up to 60-minute delays on NJ Transit, the agencies said.
The delays came as Amtrak began its second round of track renewal work at Penn Station, following track repairs over the summer. Amtrak, NJ Transit and LIRR modified their schedules to accommodate the work, which will continue until May 28.