According to the New York City Fire Department, of the 103 people with reported injuries none of them has life threatening wounds. The worst injury is a broken leg.
PHOTOS: Brooklyn train derailment
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Patients were triaged and characterized as "walking wounded," said the New York City Office of Emergency Management.
Sources told Eyewitness News that preliminary information is that the train was going too fast as it entered the station.
The train struck and went over the bumping block at the end of Track 6, and then "went by it for a few feet," said New York Gov. Andrew Gov Cuomo at a news conference.
According to the FDNY, "one of the rails actually pierced the bottom of the train ... we are fortunate we didn't have more serious injuries."
The injured were taken to Brooklyn Hospital Center, Methodist hospital and Kings County hospital.
One witness also said the train failed to come to a complete stop at the Brooklyn station. Other witnesses reported hearing a loud boom.
As the train approached the end of station, witnesses said they felt the train slam against something, and many began to panic, scream and cry.
"Typically, when you're coming into Atlantic Terminal, the train goes very slow. Today, I was saying to myself as we were coming in, it was going faster than usual," said one witness. "And before you knew it, the impact and people were, like, flying ..."
One described the aftermath as "total pandemonium," with some people falling forward and others falling on top of each other, they said.
"People crying, screaming, then it started smoking," said another witness. "So they were trying to get off the train as fast as we can because we didn't know if it was going to blow up or something like that."
An estimated 600 people were on the train when the crash occurred. Passengers were moved to the street level after the wreck.
Tracks 5 and 6 are out of service for the investigation. The LIRR said there will be residual delays for trains en route to Atlantic Terminal.
The Federal Railroad Administration (FRA) is responding to the scene.
Cuomo said in comparison with a train derailment in September in Hoboken, this crash is not as severe. He called it a "relatively minor accident."
He said it is unclear what happened to the operator, and promised a full investigation.
The MTA expects normal service for the afternoon commute with the LIRR using its five other tracks at Atlantic Terminal.
MTA Chairman Tom Prendergast said it is too early to tell what exactly caused the wreck. "Obviously, the train is supposed to stop short of the bumping block. It did not do that. So that's one of the things we will look at."
He said the partition panels and the bumping block were damaged.