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 ­emails 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 Barack 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.

Instead of disclosing the racket in 2010, Justice continued investigating for nearly four more years, so Americans and Congress didn’t know about Russian nuclear corruption at the time the deals were completed.

Obama and the Clintons defended their actions in 2015, declaring that there was no evidence that Russians had done anything wrong and there was no national security reason to oppose the Uranium One deal.

The decision to approve Rosatom’s purchase of Uranium One has been a source of political controversy since 2015, when author Peter Schweizer documented how Bill Clinton pocketed hundreds of thousands of dollars in speaking fees from Russian entities.

But FBI, Energy Department and court documents showed that the feds had gathered a mountain of evidence well before the committee’s decision that Vadim Mikerin — the top Russian overseeing Putin’s nuclear expansion inside the US — was engaged in crooked behavior starting in 2009.

Holder was also on the foreign investments committee at the time the Uranium One deal was approved — but multiple current and former government officials told The Hill they did not know whether the FBI or DOJ ever told other committee members about the crimes they had uncovered.

Evidence of the illegal conduct was gathered with the help of an American businessman who acted as a confidential witness and who began making kickback payments at Mikerin’s direction and with the permission of the FBI.

The first kickback recorded by the FBI through its informant was dated Nov. 27, 2009, the records show.

In affidavits signed in 2014 and 2015, an Energy Department agent assigned to help the FBI in the case testified that Mikerin supervised a “racketeering scheme” that involved extortion, bribery, money-laundering and kickbacks that were directed by Russia and provided kickbacks to top Russian energy officials with ties to the Kremlin, according to the report.

The case exposed a serious national security breach, The Hill reported, as Mikerin had given a no-bid contract to Transport Logistics International that transported Russia’s uranium around the US in return for more than $2 million in kickbacks from some of its executives to the Russians, court records show.