Engineering firm Bechtel National Inc. of San Francisco is building the plant to treat an estimated 56 million gallons of radioactive waste created during 50 years of nuclear weapons production.
The waste is stored in underground tanks, some of which have begun to leak, accelerating the need for the treatment plant.
A report issued after an investigation by the U.S. Energy Department said Bechtel had failed to follow procedures, maintain safety margins, train workers and correct items that did not meet requirements during construction of the plant, the Chicago Tribune reported.
Bechtel officials have denied the allegations of serious problems at the plant.
An upcoming meeting with Energy Department officials "will bring factual clarity and clear actions toward issue resolution," Bechtel officials said.
The Energy Department ordered a halt to construction at the plant this year after allegations of fundamental design and construction flaws at the treatment complex.