The President tweeted: "My thoughts and prayers are with all the victims of this morning's train collision in SC".
The Red Cross said it was sending volunteers to assist.
The Silver Star train route travels from NY to Miami, making a stop at Philadelphia's 30th Street Station on the way.
At least four cars of the freight train, which was northbound before it was parked, were crumpled, looking like crushed tin foil, but remained on the tracks. "Our hearts are with those families right now", Captain Adam Myrick, with the Lexington County Sheriff's Office, told reporters early Sunday. Palmetto Health spokeswoman Tammie Epps says 62 passengers were seen at three of its hospitals. "That has been confirmed", Harrison Cahill said. The others appeared to have minor injuries that would not require hospitalisation.
"We can't talk specifics, but of those six admissions, there were some significant injuries including some solid organ injuries and head injuries. More details to come".
Several other crash victims are reportedly in critical condition.
"It's regrettable that we have two fatalities".
The injured have been transported to local hospitals, and officials confirm everyone has been removed from the trains.
Sources with the railroad and familiar with the investigation told NBC News that before the crash, all CSX signals were offline for maintenance.
"CSX owns and controls the Columbia Subdivision where the accident occurred".
Officials confirmed there were at least two people killed and 70 injured among the 139 passengers and 8 crew. People who have questions about passengers on the train can contact us at 800-523-9101.
A deadly Amtrak train crash happened in SC early this morning around 2:30 a.m.
An Amtrak passenger train operating between NY and Miami collided with a freight train and derailed just west of Columbia, SC early Sunday morning.
Lexington County Coroner Margaret Fisher identified those killed as Michael Kempf, 54, of Savannah, Ga., and Michael Cella, 36, of Orange Park, Fla.
U.S. media reported injuries ranged from cuts and bruises to broken bones.
In December, a passenger train derailed on an overpass near Seattle, with cars crashing into the highway below, killing three people. We will also be keeping this story updated throughout the day and evening.
McMaster said the CSX train was parked on what appears to be a side track when the Amtrak train heading from NY to Miami with 139 passengers slammed into the CSX train around 2:45 a.m. Sunday near Cayce.
This photo shows passenger cars derailed after the collision. Many were treated for cuts and bruises and released, while two others were admitted to Lexington Medical Center, spokeswoman Jennifer Wilson said.
"This is not our first train derailment", said Derrec Becker of the South Caroline Emergency Management Division to the New York Times.
The National Transportation Safety Board sent investigators to the scene.