A Long Island Rail Road train running late crashed into Brooklyn’s Atlantic Terminal and was tossed off the tracks by the impact during the Wednesday morning rush hour, injuring 103 people – including some who were catapulted from their seats, officials and witnesses said.

The lead car of commuter train No. 2817 slammed into a bumper block at the end of Track 6 as it pulled into the Downtown Brooklyn transit hub about nine minutes late at 8:20 a.m. and quickly filled the station with smoke, according to officials.

The wounded all suffer ed minor injuries and dozens were treated at a makeshift triage center by emergency responders at the scene, authorities said.

Several people were pulled from the station on stretchers.

Gov. Cuomo said at a press conference at the scene that the worst injury was a woman with a “possible” broken leg.

“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, who characterized the incident as more of a crash than a derailment.

“It’s not that it derailed. The train hit the bumping block… the bumping block basically knocked it off the track,” the governor said, adding: “It was a train that didn’t stop when it was supposed to.”

The train left from the Far Rockaway terminal at 7:18 a.m. and was supposed to arrive at Atlantic Terminal – the end of the line – at 8:11 a.m., said MTA spokeswoman Nancy Gamerman.

Commuter Joey Daliapes, 21, of Long Island was in the middle car when suddenly there was a “big boom.”

“Everyone’s on the floor, smoke everywhere. I smashed my whole face into the seat in front of me…There were a lot of people bleeding, ladies crying their eyes out on the floor. We didn’t know if we were going to die.”

A woman riding in the first car of the train said, “The train suddenly slammed. We were standing and waiting to get off. One of the doors shattered and we all fell on top of each other.”

Another woman who identified herself as Raj, 45, of Queens said she noticed the train was going “a little faster” as it approached the station near the Barclays Center.

“We’re standing there, and then it was a crash. We started falling on each other,” she said.

Wendy Gerzog, 57, from Lawrence, LI, was in the first car of the train when she suddenly was under passengers who fell on top of her.

“All of a sudden it was just like boom. I was at the bottom of the pile. Everyone was screaming. It was scary,” said Gerzog, who was hospitalized with bumps and bruises.

“I couldn’t get up because my leg hurt me so bad. I couldn’t get up. I was on the floor. They had to lift me up,” she said.

Steve Miller, 46, of Park Slope was just across the platform on Track 5 waiting to catch a train into Long Island when the incident occurred.

“It was like a crashing sound – like a really loud car crash,” he said. “The train hit the end and came off the tracks. There was a screeching and the station quickly filled with dust and smoke.”

Miller said that he and other straphangers got out of the station and helped people who were getting off the train.

“My #LIRR train crashed at #AtlanticTerminal in #Brooklyn. Crazy. Seems only a few people are lightly injured,” tweeted Aaron Neufeld along with a photo of straphangers on the floor of the train and a mangled door in the terminal.

Neufeld, 26, of Long Island was sitting in the second car when mayhem broke out.

“The first car was derailed in the air. Shattered glass was on the ground and there were people with bloodied faces. One woman was wailing with blood all over her face,” he told The Post.

The train, which was carrying nearly 500 passengers, crashed through a small office space on the platform at the end of the track, wrecking it.

“That room sustained quite a bit of damage,” said FDNY Deputy Assistant Chief Dan Donoghue.

Paramedics worked on dozens injured riders above ground on the corner of Atlantic Avenue and Ashland Place.

Victims were taken to Kings County Hospital, New York Methodist Hospital and Brooklyn Hospital for treatment.

Most people self-evacuated from the train, said FDNY Commissioner Daniel Nigro.

A piece of rail pierced the bottom of the train, officials said.

“We’re actually fortunate we didn’t have more severe injuries,” Donoghue said.

A video showed the aftermath of the incident with smoke in the station as commuters rushed to leave the platform.

MTA Chairman Tom Prendergast and Cuomo said that an investigation into the crash is underway.

The speed of the train when it crashed was not immediately known and Prendergast noted that the when trains enter the terminal the standard speed is between 10 and 15 mph.

Cuomo called the incident a “relatively minor accident.”

Wednesday’s LIRR incident came a little more than three months after the deadly New Jersey Transit crash at Hoboken Terminal.

Commuter Fabiola Bittar de Kroon, 34, was killed by falling debris on the platform after Train 1614 barreled into the station on Sept. 29.

“This is minor compared to what happened in Hoboken,” the governor said.

The National Transportation Safety Board is sending investigators to the scene.

Train service is expected to resume in the afternoon.

Additional reporting by Sophia Rosenbaum and Stephanie Pagones