There are 103 people with reported injuries. According to the New York City Fire Department, none of the injuries is life threatening.
Eleven people had to be removed by stretcher, and the worst injury was a broken leg. Patients were triaged and characterized as "walking wounded," said the New York City Office of Emergency Management.
The train struck and went over the bumping block at the end of Track 6, then "went by it for a few feet," said New York Gov. Andrew Gov Cuomo at a news conference. "This was minor compared to Hoboken."
Sources told Eyewitness News that preliminary information is that the train was going too fast as it entered the station.
"One of the rails actually pierced the bottom of the train," said FDNY Deputy Assistant Chief Daniel Donoghue. "We are fortunate we didn't have more serious injuries."
The train came to rest against a small room at the end of the track.
"It actually hit that wall pretty hard," Donoghue said. "That room sustained quite a bit of damage."
As the train got to the station, witnesses said they felt it slam against something, and many began to panic, scream and cry. Other witnesses reported hearing a loud boom.
"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 witness described the aftermath as "total pandemonium," with some falling forward and others falling on top of each other.
"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."
The train left Far Rockaway at 7:18 a.m. and was supposed to arrive at Atlantic Terminal at 8:11 a.m. The accident occurred around 8:20 a.m.
An estimated 430 people were on the train when the crash occurred. Passengers were moved to the street level after the wreck.
Tracks 5 and 6 were out of service for the investigation, but the MTA expects normal service for the afternoon commute with the LIRR using its five other tracks at Atlantic Terminal.
Around noon, the LIRR reported that trains in and out of Atlantic Terminal were on or close to schedule.
Gov Cuomo on scene of this morning's LIRR accident pic.twitter.com/r2KK1QytWC— Melissa DeRosa (@melissadderosa) January 4, 2017
Cuomo said it is unclear what happened to the operator and promised a full investigation.
In comparison with a fatal train derailment in September in Hoboken, this crash is not as severe, Cuomo said. He called it a "relatively minor accident."
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.
Prendergast said the partition panels and the bumping block at the station were damaged.
WATCH: N.J. Burkett describes scene at Atlantic Terminal after LIRR crash:
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