Authorities are investigating the derailment but ruled out possibility of any criminal activity.
A Metro-North train from Poughkeepsie bound for the Grand Central station in Manhattan derailed just a few feet away from the Harlem River in the Bronx.
Four cars on the seven-car train turned on their side, throwing unsuspecting passengers into the air and critically injuring several.
Authorities said the derailment happened as the train was rounding a curve north of the Spuyten Duyvil station.
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Firefighters and rescue teams were searching the Harlem river water for victims as other first responders carried out search and rescue operations.
New York Governor Andrew Cuomo had reached the site of the accident to take stock of the rescue efforts.
While law enforcement officials have ruled out suspicion of any criminality, Metropolitan Transportation Authority spokeswoman Marjorie Anders said the train's black box would provide information about how fast the train was travelling.
MTA Chairman Thomas Prendergast told reporters that the speed of the train and whether it was running was travelling faster than it should would be investigated.
A passenger on the train, Frank Tatulli, told Eyewitness News that the train was travelling at a speed higher than normal. Tatulli said he got out of the train on his own, and suffered head and neck injuries.
Another passenger Joel Zaritsky said he was sleeping on the train and woke up when the car "started rolling several times. Then I saw the gravel coming at me, and I heard people screaming. There was smoke everywhere and debris. People were thrown to the other side of the train.