The MTA has yet to assess the damage to the tracks.
The MTA says it happened Monday at 6:09 p.m. just east of the platforms at Penn Station as the train was entering the East River Tunnel.
The 10-car train was moving at a slow speed as it was entering the tunnel. The MTA says it derailed.
The train involved was the 5:51 p.m. from Penn Station, due in Hempstead at 6:46 p.m.
There are no reports of injuries.
The MTA estimates there were 800 to 1,000 people on the train.
They had to be evacuated by emergency workers.
Passengers in the rear five cars were able to walk through the train and evacuate.
Another train was brought alongside for passengers in the front five cars to disembark. It took two hours to get everyone off the train.
Passenger Tameka Chandler, of Queens, said she was in the eighth of 10 cars. She said when the train got into the tunnel, it started to shake and rock and she could see the car ahead of hers tilted to one side before it derailed.
"It was sideways," she said.
The passengers remained calm, Chandler said.
"People were looking around, but it wasn't chaotic," she said.
One out of the four East River Tunnels was out of service for the remainder of the evening rush hour.
Customers experienced expect delays as well as some cancellations.
Westbound service into New York City was suspended to allow trains to head east using the three remaining tunnels.
Amtrak trains were moving, but delays up to 60 minutes occurred for passengers traveling north of New York toward Boston.
Passengers traveling in other directions experienced lesser delays as a result of the train congestion at the station.
(Some information from the Associated Press)