The Obama administration knew that Russia had used bribery, kickbacks and extortion to get a stake in the US atomic-energy industry — but cut deals giving Moscow control of a large chunk of the US uranium supply anyway, according to a report Tuesday.

The FBI used a confidential US witness working inside the Russian nuclear industry to gather records, make secret recordings and intercept ­e-mails as early as 2009 that showed the Kremlin had compromised an American uranium trucking company, The Hill reported.

Executives at the company, Transport Logistics International, kicked back about $2 million to the Russians in exchange for lucrative no-bid contracts — a scheme that violated the Foreign Corrupt Practices Act, the report said.

The feds also learned that Russian nuclear officials had gotten millions of dollars into the US designed to benefit the Clinton Foundation at the same time then-Secretary of State Hillary Clinton served on a government committee that signed off on the deals, sources told The Hill.

The racketeering operation was conducted “with the consent of higher-level officials” in Russia who “shared the proceeds” from the kickbacks, an agent later stated in an affidavit.

But the Justice Department under Attorney General Eric Holder did not bring charges in the case prior to the deals being cut.

At the time, President Obama and Clinton’s State Department were trying to “reset” relations between the two nuclear rivals — an effort that largely failed.

The first deal was wrapped up in October 2010 when the State Department and the Committee on Foreign Investment agreed to sell part of Uranium One, a Toronto-based mining giant with operations in Wyoming, Australia, Canada, Kazakhstan, South Africa and elsewhere, to the Russian nuclear company Rosatom.

The move gave the Russians control over roughly 20 percent of the US uranium supply — and gave Russian strongman Vladimir Putin a large and profitable stake in the US atomic-power industry.

When Donald Trump slammed Clinton on the campaign trail in 2016 over the sale, her spokesman said she was not involved in the committee review and that the State Department official who handled it said she “never intervened . . . on any [committee] matter.”

In the second deal, in 2011, Obama gave the OK for Rosatom’s Tenex subsidiary to sell the Canadian company’s uranium to American nuclear power plants.

Before, Tenex could only sell reprocessed uranium from dismantled Soviet nuclear weapons to power plants in the US.

“The Russians were compromising American contractors in the nuclear industry with kickbacks and extortion threats, all of which raised legitimate national-security concerns. And none of that evidence got aired before the Obama administration made those decisions,” a source told the paper. Continue reading.