The incident occurred on the subway track that runs above West 6th Street between 8th Street and Neptune Avenue stations just before 12:30 p.m.
The MTA worked to move the train that derailed and inspect the tracks where the derailment occurred.
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After the train derailed, rescue cars evacuated 37 people, including workers, within an hour. No injuries were reported.
"The train just shook, and it went up on its side, so that's what it felt like. So, I knew right away it was a derailment. I've never experienced it before, but it was obvious," said Gregory Perelshteim, a passenger on the F train.
The train was coming into the Neptune station at the time of the incident.
The cause of the derailment was not immediately made clear. Transit authority officials said the railcar was relatively new and the investigation is now focused on the tracks themselves.
"The track needs to be straight in order for the train to run on top of it safely and without a slow speed derailment," NYC Transit President Richard Davey said.
One photo exclusively obtained by Eyewitness News appears to show rails that were misaligned at the point of the derailment.
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There was no F train service between Avenue X and Coney Island as of Wednesday night.
The service disruption came less than a week after two dozen people were injured when a No. 1 train derailed in Manhattan Thursday.
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"Look, we'll get to the bottom of this. I realize that we had issues, obviously, last week, as well, and we'll get to the bottom of whatever this is. But at this point, from the incident we had last week and derailment today, don't seem like they're connected at all," said Transit Authority President Rich Davey.
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