The Department of Energy is holding Savannah River Nuclear Solutions responsible for an acid spill and an electrical accident that injured workers in 2009.
It's the contractor responsible for radioactive cleanup at the site.
The company will have to pay $3 million.
The DOE has also fined Parsons Infrastructure and Technology $70,000 for a separate 2009 accident involving a crane, which caused a worker to lose three of his fingers.
Site officials say safety programs at SRS have been improved since the accidents.