Amtrak spokesman Mike Tolbert said earlier Saturday that train service in or out of the city was halted as crews investigated overhead power issues.
Amtrak crews are investigating what caused those power issues.
Amtrak and New Jersey Transit service on the Northeast Corridor in and out of New York Penn Station resumed Saturday after brief delays, but officials warned additional delays are possible.
When the first rescue train couldn't reach the stalled train, a second locomotive was sent in and towed everyone to safety after about two hours. "And then sent another vehicle in to rescue us, to pull us out, and there was a problem with that auto", one passenger recalled.
Amtrak travel between NY and New Jersey was briefly suspended, but had resumed on Amtrak rails by 1:15 p.m.
After 20 minutes, a rescue train brought the train back to the station, where passengers safely disembarked, an Amtrak spokesman said.
That also led to train delays until about 5 p.m., he said.
"Summer of Hell", begins for commuters with day one of Penn Station repairs underway on Monday, July 10, 2017.
Lhota says transit officials and commuters are "getting through this together". "I'd like to start by thanking the passengers of Amtrak, Long Island Rail Road, and New Jersey Transit", Amtrak Chief Operating Officer Scot Naparstek said.
The trouble began when a train from Miami carrying 165 people stalled as it entered Penn Station about 11:50 a.m.
The overhead power concern will continued to be monitored, he added.
That was the third NJ Transit derailment at the station since March.
As we approach the end of week one of summer track repairs at Penn Station, Amtrak says the emergency track work is slightly ahead of schedule.