The FDNY initially said dozens of people suffered non-life-threatening injuries, and all of those injured were treated at the scene, NBC New York reported. There will be delays "into and out of Atlantic Terminal", the railroad tweeted.
The NTSB and the Federal Railroad Administration sent federal investigators to the scene. The incident happened on LIRR track 6 around 8:15 a.m, the MTA said.
Cuomo said in comparison with a train derailment in September in Hoboken, this crash is not as severe.
Atlantic Terminal, formerly known as the Flatbush Avenue station, is the westernmost stop on the Long Island Rail Road's Atlantic Branch.
A passenger on the train described the accident to WNBC, claiming she heard a loud boom, then the train doors opened. The MTA expects normal service for the afternoon commute with the LIRR using its five other tracks at Atlantic Terminal.
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The lead vehicle was derailed, Prendergast told reporters.
One woman riding the train told news reporters outside the station that the sudden impact of the derailment caused havoc inside her rail vehicle.
"We'll have an investigation as to why the operator didn't stop the train before it hit the bumping block, but that's where we are at this time", said Cuomo.
The derailment comes months after a commuter train crashed into a station hub in Hoboken, New Jersey killing one person. Any rail employees with "safety-sensitive" jobs who exhibit sleep apnea symptoms are removed from operation until they can certify that the condition has been corrected or controlled. Also onboard that train were about 600 passengers when it came into contact with a maintenance train on a neighboring track.