SEATTLE — Bechtel National Inc. and a subcontractor have agreed to pay $125 million to settle a lawsuit alleging subpar work in building a nuclear waste treatment facility on the Hanford Nuclear Reservation in Washington state, along with accusations that Bechtel illegally used taxpayer money for lobbying.

The settlement, filed Wednesday in U.S. District Court in Spokane, resolves a lawsuit initially brought in 2013 by three whistleblowers — managers at the nuclear site who sued on behalf of the federal government because they worried about safety issues at the Hanford Waste Treatment Plant.

The waste is currently stored in aging underground tanks, dozens of which are leaking, threatening the Columbia River nearby.

Once completed, the multibillion-dollar facility is supposed to convert 56 million gallons of radioactive nuclear waste left over from the government's nuclear weapons program into glass for safe storage deep underground. But in joining the whistleblowers' lawsuit, the U.S. Justice Department said that for 13 years, Bechtel and subcontractor URS Corp. knowingly charged the Department of Energy for materials and services that failed to meet rigorous standards for nuclear facilities.

The government's investigation showed that the companies "recklessly purchased deficient materials and services with taxpayer money," said Spokane U.S. Attorney Michael Ormsby, which he called "deeply concerning given the obvious importance of nuclear safety" at the plant.

"The money allocated by Congress for the Waste Treatment Plant is intended to fund the Department of Energy's important mission to clean up the contaminated Hanford nuclear site, and this mission is undermined if funds are wasted on goods or services that are not nuclear compliant or to further lobbying activities," Benjamin C. Mizer, the head of the Justice Department's Civil Division, said in a news release.

The settlement also resolves accusations Bechtel, a giant engineering and construction company, illegally used taxpayer dollars to fund a multiyear lobbying campaign. Bechtel paid lobbyists to downplay to members of Congress the significance of concerns raised by an independent federal oversight board, prosecutors said.

The companies denied any wrongdoing in the settlement.

"We have performed our work at the WTP project ethically and professionally," Bechtel spokesman Fred deSousa said in an emailed statement. "A protracted legal proceeding and the distraction of a trial are not in the best interest of the WTP project. Instead, we will focus on continuing to work in collaboration with the Department of Energy to solve the most challenging and complex radioactive waste problem in U.S. history."

Bechtel will pay $67.5 million to the federal government, while URS will pay $57.5 million of the settlement. For bringing the suit, the whistleblowers, who said they were retaliated against or even fired for raising safety concerns, are entitled to keep 15 to 25 percent of the total payout, said Joe Harrington, a spokesman for the U.S. Attorney's Office.

Hanford, located in south-central Washington state, for decades made plutonium for nuclear weapons. The site is now engaged in cleaning up the nation's largest collection of nuclear waste.

Tom Carpenter, executive director of the watchdog group Hanford Challenge, called the settlement "justice being served."

"This is a company that probably should not be working for the government," he said. "It started by harassing and silencing whistleblowers, and when they brought their information public, it caused the work at the plant to be suspended."