The engineer applied the emergency brakes five seconds before impact, the National Transportation Safety Board said late Monday. No one on board was killed, although more than 30 passengers were injured.
Videos showed construction equipment on the track and a contractor's equipment on an adjacent track before the crash Sunday morning, NTSB investigator Ryan Frigo said.
He could not comment on who was authorized to be there, but said work crews were scheduled to be interviewed on Tuesday.
Amtrak issued a statement Monday night saying it was "deeply saddened" by the deaths of the two workers and the injuries suffered by passengers. It said it was working with the NTSB to "identify the issues that led to this incident."
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Amtrak trains on the Northeast Corridor resumed regular service on Monday.
The train was heading from New York to Savannah, Georgia, at about 8 AM Sunday when it hit a piece of equipment in Chester, about 15 miles outside of Philadelphia. The impact derailed the lead engine of the train, which was carrying more than 300 passengers and seven crew members. The injuries were not considered life-threatening.
The union representing Carter said a total of three workers have now been killed on the job on Amtrak's Northeast Corridor since March 1. And that raises questions about worker safety, the Brotherhood of Maintenance of Way Employees said.
Amtrak introduced a set of new safety protocols effective March 15. It says violations are handled with zero tolerance, and some cases lead to immediate dismissal.
Rail safety workers said track workers are supposed to double-check their assignments with dispatchers to be sure they are not working on or around an active track.