A New York City commuter train derailed at a Brooklyn terminal after ramming into a bumper during Wednesday’s morning rush hour, leaving more than 100 people with non-life-threatening injuries, city officials said.

Dozens of emergency crews swarmed Atlantic Terminal after the Long Island Railroad train went off the tracks inside the busy transportation hub at about 8.30am local time, the New York City Fire Department said.

The train failed to stop on time and struck a bumping block at a fairly low rate of speed, which caused it to derail, New York Governor Andrew Cuomo said at a briefing at the crash site.

About 103 people were injured in the accident, the New York Fire Department said in a Twitter message.

Earlier Deputy Assistant Chief Dan Donoghue said at the briefing that 11 people had to go to the hospital.

Fire Department staff treat injured passengers after the accident. Photo: AAP.

The derailment, which severely damaged the train’s front two cars, was the second major accident involving New York City’s commuter railroads in the past three months.

In late September, a New Jersey train crashed into a terminal in Hoboken, killing one woman and injuring 114 people, including the engineer.

Mr Cuomo, who has made infrastructure improvements a centrepiece of his agenda, said Wednesday’s incident was minor in comparison.

The most serious injury in the crash was a broken leg, he said.

“There was an extensive damage in Hoboken,” Cuomo said.

That train was coming in much faster, did much much more damage.

In Brooklyn, police and firefighters, some holding stretchers, were entering the terminal as emergency vehicles blocked traffic.

Commuters, meanwhile, described a frightening and chaotic scene on social media.

“People flying everywhere,” Serena Janae, who said she was a passenger on the derailed train, wrote on Facebook.

The US Federal Railroad Administration and the National Transportation Safety Board said they were sending investigators to the scene.

Atlantic Terminal, which also connects commuters to nine city subway lines, is one of New York’s busiest stations.