New Jersey Governor Chris Christie said the train entered the station at Hoboken "at a high rate of speed" and "crashed through the barriers, bringing it into the interior wall" of the terminal.
A woman who was standing on the platform was hit and killed by debris from the crash, Christie told the news conference. She was the only confirmed fatality.
The train's driver was in serious condition and being treated at a local hospital but was cooperating with the crash probe, he said.
"We have no indication that this is anything but a tragic accident," Christie said, adding that an investigation was underway.
Video and photos on social media showed major damage to the transit choke point just over the Hudson river from Manhattan, with the train tangled in wires and debris from what appeared to be caved in portions of the roof.
The Hoboken terminal is a major transfer point for New Jersey trains and buses, as well as ferries and the PATH commuter train that take passengers to New York.
People examine the wreckage of a New Jersey Transit commuter train that crashed into the train station during the morning rush hour in Hoboken (AAP) Source: AAP
'Difficult times'
Kenneth Garay, chief medical officer at Jersey City medical center, said its surgeons were "all hands on deck" as they treated patients suffering from broken bones internal injuries and lacerations.
"None at this point are life-threatening. They're critical and stable and being carefully monitored," he told CNN.
Garay said that another 40 people were transported from the train station by bus to be treated for "walking types of injuries."
Christie said he had been contacted by the White House and was working with federal, state and local authorities to "make sure this investigation is seamless and coordinated."
Democratic presidential candidate Hillary Clinton said she "was terribly upset this morning."
Twitter user Cephster has given permission for AP to use this photo of the train crash in Hoboken, New Jersey on Sept. 29, 2016 (AAP) Source: Twitter
"It's a horrible accident," the former New York senator said at a campaign rally in Des Moines, Iowa. "I just want to send our thoughts and prayers."
Donald Trump also expressed his sympathies with the victims on Twitter.
"My condolences to those involved in today's horrible accident in NJ and my deepest gratitude to all of the amazing first responders," the Republican candidate said.
Alongside Christie was New York Governor Andrew Cuomo, who canceled his trip to Israel for the funeral of Peace Prize Winner Shimon Peres.
"These are difficult times over these past weeks and months, between terrorist attacks and natural disasters," said Cuomo, referring to a recent string of bombings in New York in New Jersey.
'Pretty chaotic'
Train #1614 was arriving from Spring Valley, New York when it struck the Hoboken terminal building at around 8:45 am (1245 GMT), New Jersey Transit said in a statement.
Emergency vehicles converged on the scene in response to the crash.
Passengers described a scene of chaos with dazed and bloodied people making their way to safety.
"We crashed, and the lights went out. A few people screamed," Leon Offengenden told CNN.
"It was pretty chaotic. And people just in shock and everybody has photos and cameras out and iPads. It was pretty intense," he said.
Passengers described the train -- which was carrying around 250 people -- ramming at full speed into the bumper at the end of the track.
"We never slowed down," Jim Finan, a commuter from New Jersey, told Fox News. "We ploughed, I mean, right through the bumper."
Michael Larson, a transit employee, told reporters he heard a "bomb-like explosion" as the train hit the concrete bumpers with such force that it went airborne.
"It went up and over the bumper block, through the depot... and came to rest at the wall by the waiting room."
Investigators will be looking for similarities with a 2011 PATH commuter train crash at Hoboken that injured several dozen people, Bella Dinh-Zarr, vice chairwoman of the National Transportation Safety Board, told reporters.
"We are going to hit the ground running," she said.
Christie said engineers were examining the structural integrity of the Hoboken terminal, which underwent lengthy repairs after being hit during Superstorm Sandy in 2012.
The last major train crash in the United States was in May 2015, when an Amtrak train linking Washington to New York derailed in Philadelphia, leaving eight dead and 200 injured.
In December 2013 in New York a suburban train derailed in the Bronx while traveling at several times the speed limit, leaving four people dead and more than 60 injured.
