An investigation is currently underway on how an Amtrak passenger train ended up on the wrong track, causing a deadly crash with another train early Sunday morning in the U.S. state of South Carolina.

Two Amtrak employees were killed and more than 100 were injured as the passenger train collided into a CSX freight train.

An aerial view of the site of an early morning train crash Sunday, Feb. 4, 2018 between an Amtrak train, bottom right, and a CSX freight train, top left, in Cayce, SC. [Photo: AP]

An aerial view of the site of an early morning train crash Sunday, Feb. 4, 2018 between an Amtrak train, bottom right, and a CSX freight train, top left, in Cayce, SC. [Photo: AP]

"It appears that Amtrak was on the wrong track," South Carolina Governor Henry McMaster said at a press conference.

The CSX train was parked on a side track when the Amtrak train, heading from New York to Miami, slammed into it at about 59 mph (95 km/h), he said.

The freight train engines were "all torn up" and the Amtrak engine was "barely recognizable" from the crash.

Investigators are now focused on why a railroad switch was set in the wrong position, leading to the Amtrak train off the main line and onto the side track which was occupied by the empty CSX train.

"For whatever reason that switch was, as they say in the railroad industry, 'lined and locked,'" said Robert Sumwalt, chairman of the National Transportation Safety Board. "Which basically means it was aligned for the train coming this way to be diverted into the siding."

"Key to this investigation (is) why that switch was lined that way," Sumwalt said at a press conference Sunday afternoon.

It will take several months to determine the cause of the crash, Sumwalt said.

The Lexington County coroner identified the two dead as engineer Michael Kempf, 54, and conductor Michael Cella, 36, who were riding in the front of the train.

The Amtrak train consisted of seven passenger cars and one locomotive, while the CSX train comprised two locomotives and 34 empty "autorack" cars for transporting automobiles, local media reported.

The U.S. Transportation Department said in a statement that it has sent officials to the crash site and tried to work out ways to "ensure a safe and reliable rail system going forward."

Earlier in the day, Amtrak CEO Richard Anderson said the signalling system was not operating, which is why trains were being directed through the corridor manually by CSX dispatchers.

CSX owns and controls the Columbia Subdivision tracks where the crash occurred and is responsible for overseeing the dispatching of trains and signal systems, local media reported quoting Anderson.

Earlier, local authorities said about 5,000 gallons of fuel were spilled following the train crash.

However, Lexington County spokesman Harrison Cahill said there was "no threat to the public at the time."

Amtrak said Sunday morning that there were eight crew members and approximately 139 passengers in the train when the crash happened.

It is the third deadly wreck involving Amtrak in about two months.

In December, an Amtrak train derailed in the northwestern U.S. state of Washington, killing three people and injured dozens. Last week, an Amtrak train carrying Republican lawmakers to a retreat in West Virginia hit a garbage truck in Virginia, leaving one dead and two seriously injured.