The front of the slow-moving train hit a bumping block as it pulled into Atlantic Terminal, left the tracks and smashed into a small structure, apparently a work area; a rail pierced the floor of a train car, authorities said.
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About 100 people were treated for minor injuries after the 8:30 a.m. crash; many had been standing as they prepared to get off the train at the last stop.
Some people were removed on stretchers. Others sat, stunned, on the pavement outside - bleeding, holding ice packs on their heads, rising and limping away with help from rescuers.
"The entire structure started shaking," said Steben Medina, who was having coffee at the terminal when he heard the crash and screams. "I thought a bomb had gone off or something."
The most serious injury, though, appeared to be a broken leg, said Mayor Bill de Blasio.
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"Luckily ... all things considered, this was a relatively minor accident," said Gov. Andrew Cuomo.
The terminal is beneath a shopping mall in downtown Brooklyn, adjacent to the Barclays Center, home to Nets basketball, Islanders hockey and major concerts.
A similar accident across the harbor in Hoboken, New Jersey in September was much worse. There, a New Jersey Transit commuter train plowed off the end of a track, killing a woman standing in the station. Federal investigators are examining whether a more modern bumper or other barriers could have made a difference.
The train in Wednesday's wreck originated in the Far Rockaway section of Queens and was carrying around 450 people, officials said.
"People just went flying," passenger Donette Smith told The New York Times. "It was very scary."
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"I sort of slammed into the folks who were facing me," said Audrey Foster, who was sitting in the second car and hurt her side.
Foster said there were a lot of familiar faces on her daily commute, and many of those people were injured. "It's just sad," she said.
The National Transportation Safety Board dispatched investigators.
Metropolitan Transportation Authority Chairman Thomas Prendergast said there is "a signal system that controls it coming in at limited speeds. But when you're getting to the end it's the locomotive engineer's responsibility. And the train's brakes have to work. All those things have to be looked at in the investigation."