Two people were killed - Amtrak employees Michael Kempf, 54, and Michael Cella, 36, who were both in the train's first auto at the time of the crash.
The Transportation Department said Secretary Elaine Chao also is sending her senior adviser, Jim Ray, to the crash site.
The train then continued on its route toward Columbia on its way to its final destination in Miami, Florida. Two of those passengers were admitted.
Palmetto Health hospitals confirmed they received a total of 62 patients.
CSX issued a statement expressing condolences but said nothing about the cause of the accident.
"It's unfortunate that we have two fatalities". Engineer Michael Kempf, 54, of Savannah, Ga.; and Conductor Michael Cella, 36, of Orange Park, Fla. Two Amtrak crew members were killed, and more than 100 people were injured.
"We should have had a lot more casualties, but we didn't", said Lexington County coroner Margaret Fisher, who identified the dead at an afternoon news conference. He says the injuries ranged from scratches to broken bones.
The governor of South Carolina, Henry McMaster, said in a news conference that the CSX train was on the a loading track when the Amtrak, which had 147 people on board, smashed into it after 2 a.m. local time in Cayce, ABC News reported.
He described the freight train engines as "all torn up", and the Amtrak engine as "barely recognizable" from the impact. The National Transportation Safety Board has propelled an examination, which is relied upon to be finished in a year and a half.
Sumwalt said that positive train control - a GPS-based safety system that can automatically slow or stop trains - could have prevented the accident. Both men were in the first auto of the train.
He says the freight train crew took the CSX train from one side track across the main line and back to another side track after unloading automobiles.
"We are cooperating fully with the NTSB, which is leading the investigation, as well as working with FRA and CSX", Amtrak said. Amtrak has set up a hotline where family can get information about people involved: 1-800-523-9101. Officials are estimating about 5,000 gallons of fuel has spilled. "My thoughts and prayers are with all of the victims involved in this mornings (sic) train collision in SC", he tweeted.
This is the third Amtrak crash since December.
Last week, an Amtrak train carrying members of Congress to a Republican retreat in West Virginia struck a truck near Charlottesville, Virginia.
This story will be updated throughout the day. No serious injuries were reported for anyone on the train, and some lawmakers with medical experience offered assistance at the scene.