The Energy Department has repeatedly and substantially underestimated the costs of building a South Carolina plant meant to turn surplus plutonium from nuclear weapons into fuel for power plants, federal auditors declared in a new report on Feb. 20.

The Government Accountability Office said the DOE’s National Nuclear Security Administration moreover has never completed “root cause analyses” of why the cost of the two construction projects at the heart of the effort have ballooned over the past decade.

Providing a new window on what it depicted as the agency’s continuing mismanagement of the program, the GAO said that without such analyses, those in charge can’t correct existing problems, weigh any alternatives and learn from past mistakes.

The department failed to take a deep dive into the numbers, the report said, even when NNSA officials decided last April to slow construction of the Mixed Oxide or MOX fuel plant, which is located at DOE’s Savannah River Site, pending a review of alternatives for disposing of the plutonium.

NNSA officials have repeatedly promised to reform construction management of the overall project, which includes not only the fuel plant — which combines plutonium and uranium oxides to make reactor fuel — but a separate building where nuclear wastes are solidified to get them ready for burial.

The MOX plant is now expected to cost billions more than first estimated, due to what the GAO last year called the Energy agency’s “record of inadequate management and oversight.”

The GAO report found that the Energy department’s April 2013 draft estimate of the total cost of the plutonium weapons-to-fuel program — $24.2 billion — was “not reliable” because it ignored key steps in calculating the figure.

A recently-completed Energy Department study of the plutonium plant and alternatives, not yet released, pegs the overall cost of the project at up to $35 billion, the Center for Public Integrity has reported.

Auditors said in Thursday’s report that the NNSA’s April figure was based on a review marred by the lack of any written plan, as well as a failure to document the sources of its data or submit its estimates to management for approval.

NNSA officials told the GAO, the report said, that they regarded its $24.2 billion figure as “predecisional” because the whole program was under review at the time and they thus had no need to get management to sign off on it. NNSA also did not obtain an independent estimate for the overall program costs, the report said, nor did it seek similar estimates for the fuel plant and waste solidification building.

In 2002, the Energy agency estimated the MOX plutonium fuel plant alone would cost about $1 billion. By 2012 it said it would cost $7.7 billion. Now the Energy agency expects the price to rise to up to $10 billion, according to a government official who has studied the project.

In a Jan. 24 response to the GAO, NNSA’s Associate Administrator for Management and Budget Cynthia Lersten concurred with most of the findings, and wrote that “root cause analyses” for cost increases at the MOX plant and Waste Solidification Building are expected to be completed by Sept. 30.

She also wrote that the agency wouldn’t formally update its MOX project cost estimates until after the Obama administration decides whether to proceed with it or select an alternative pathway to rendering the plutonium in nuclear weapons unusable.

But GAO’s report said that DOE never mentioned that it was conducting a root cause analysis during its review of the program, which began in November 2012 and ended in January.

Under a 2000 treaty, both the United States and Russia have pledged to dispose of 34 tons each of their plutonium from dismantled warheads. At Russia’s insistence, the United States agreed to do so by turning it into reactor fuel.

The NNSA did not immediately respond to a request for comment.