The cause of the collapse was not immediately known.
The collapse was discovered during a routine inspection, the agency said.
The latest estimate to finish the overall cleanup of Hanford is more than $107 billion and the work would take until 2060. Hanford said there's no indication of a release of contamination and no reports of injuries. Nearby workers were evacuated.
A former Energy Department official Bob Alvarez said that the rail cars carry spent fuel from a reactor area long the river to the chemical processing facility, which then extracts risky plutonium and uranium.
Reports are not now indicating any release of radioactivity.
"My thoughts are with the first responders who are working to assess the situation on the ground", she said.
But the plant's construction has been halted by design and safety concerns.
The Energy Department says no one was injured in the collapse and no radiation has been released.
The Department of Energy said "Secretary [Rick] Perry has been briefed on the incident [and] the Department will continue to monitor this closely".
The US Department of Energy said it activated its emergency operations protocol after reports of a "cave-in" at the 200 East Area in Hanford, home to numerous solid waste sites about 200 miles from Seattle. It connects to a PUREX (plutonium uranium extraction) building.
The area contains about 56 million gallons (211.98 million liters) of radioactive waste, most of it in 177 underground tanks. The breached tunnel was used to "bury radioactive waste from the production of plutonium", Inslee said.
The US Department of Energy downplayed the incident at the time saying the leak had been "anticipated" amid ongoing efforts to empty the tank.
The Trump administration has proposed increasing spending on nuclear waste management, even as it plans to slash other parts of the department's budget. Hanford made the plutonium for the atomic bomb that was dropped on Nagasaki, Japan, and much of the plutonium for the nation's nuclear arsenal.