WASHINGTON — Before Saudi Arabia’s crown prince, Mohammed bin Salman, was implicated by the C.I.A. in the killing of Jamal Khashoggi, American intelligence agencies were trying to solve a separate mystery: Was the prince laying the groundwork for building an atomic bomb?

The 33-year-old heir to the Saudi throne had been overseeing a negotiation with the Energy Department and the State Department to get the United States to sell designs for nuclear power plants to the kingdom. The deal was worth upward of $80 billion, depending on how many plants Saudi Arabia decided to build.

But there is a hitch: Saudi Arabia insists on producing its own nuclear fuel, even though it could buy it more cheaply abroad, according to American and Saudi officials familiar with the negotiations. That raised concerns in Washington that the Saudis could divert their fuel into a covert weapons project — exactly what the United States and its allies feared Iran was doing before it reached the 2015 nuclear accord, which President Trump has since abandoned.

Prince Mohammed set off alarms when he declared earlier this year, in the midst of the negotiation, that if Iran, Saudi Arabia’s fiercest rival, “developed a nuclear bomb, we will follow suit as soon as possible.” His negotiators stirred more worries by telling the Trump administration that Saudi Arabia would refuse to sign an agreement that would allow United Nations inspectors to look anywhere in the country for signs that the Saudis might be working on a bomb, American officials said.

Asked in Congress last March about his secret negotiations with the Saudis, Energy Secretary Rick Perry dodged a question about whether the Trump administration would insist that the kingdom be banned from producing nuclear fuel.

Eight months later, the administration will not say where the negotiations stand. Now lurking behind the transaction is the question of whether a Saudi government that assassinated Mr. Khashoggi and repeatedly changed its story about the murder can be trusted with nuclear fuel and technology. Such fuel can be used for benign or military purposes: If uranium is enriched to 4 percent purity, it can fuel a power plant; at 90 percent it can be used for a bomb.

Privately, administration officials argue that if the United States does not sell the nuclear equipment to Saudi Arabia someone else will — maybe Russia, China or South Korea.

They stress that assuring that the Saudis use a reactor designed by Westinghouse, the only American competitor for the deal, fits with Mr. Trump’s insistence that jobs, oil and the strategic relationship between Riyadh and Washington are all far more important than the death of a Saudi dissident who was living, and writing newspaper columns, in the United States.

Under the rules that govern nuclear accords of this kind, Congress would have the opportunity to reject any agreement with Saudi Arabia, though the House and Senate would each need a veto-proof majority to stop Mr. Trump’s plans.

“It is one thing to sell them planes, but another to sell them nukes, or the capacity to build them,’’ said Representative Brad Sherman, Democrat of California and a member of the House Foreign Affairs Committee.

Following Mr. Khashoggi’s death, Mr. Sherman has led the charge to change the law and make it harder for the Trump administration to reach a nuclear agreement with Saudi Arabia. He described it as one of the most effective ways to punish Prince Mohammed.

“A country that can’t be trusted with a bone saw shouldn’t be trusted with nuclear weapons,” Mr. Sherman said, referring to Mr. Khashoggi’s brutal killing in the Saudi Consulate in Istanbul last month.

Nuclear experts said Prince Mohammed should have been disqualified from receiving nuclear help as soon as he raised the prospect of acquiring atomic weapons to counter Iran.

“We have never before contemplated, let alone concluded, a nuclear cooperation agreement with a country that was threatening to leave the nonproliferation treaty, even provisionally,” said William Tobey, a senior official in the Energy Department during the Bush administration who has testified about the risks of the agreement with Saudi Arabia.

He was referring to the crown prince’s threat to match any Iranian nuclear weapon — a step that would require the Saudis to either publicly abandon their commitments under the nonproliferation treaty or secretly race for the bomb.

The Trump administration declined to provide an update on the negotiations, which were intense enough that Mr. Perry went to Riyadh in late 2017. Within the last several months, a senior State Department official engaged in further discussions over the deal in Europe.

The Saudi energy ministry said in a statement: “The Saudi government has repeatedly confirmed that every component of the Saudi atomic energy program is strictly for civil and peaceful uses. The Saudi government has decided to move with this project not only to diversify energy sources but also to contribute to our economy. Saudi Arabia has repeatedly called for a Middle East free from all forms of nuclear weapons.”

Saudi Arabia has long displayed interest in acquiring, or helping allies acquire, the building blocks of a program that could make nuclear weapons and protect the kingdom from potential threats from its neighbors — first Israel, then Iraq and Iran.

The Saudi government provided the financing for Pakistan to secretly build its own nuclear arms, the first “Sunni bomb,” as the Pakistani creators of the program called it. That financial link has long left American intelligence officials wondering if there was a quid pro quo: that if Saudi Arabia ever needed its own small arsenal, Pakistan could provide it — perhaps by moving Pakistani troops to Saudi territory.

The Saudis were also thinking of delivery systems. In 1988, the kingdom bought medium-range missiles from China that were designed to be fitted with nuclear, chemical or biological warheads, drawing protests from American officials.

Riyadh’s worries spiked in 2003 when it was revealed that Tehran had secretly built a vast underground plant for enriching uranium — a fuel for nuclear arms and reactors.

Back then, the Iranians made the same argument that the Saudis are currently making: that they needed to possess all of the production facilities necessary for fueling nuclear power plants. (The Iranians in 2011 opened one such plant, a nuclear reactor at Bushehr, built by the Russians.)

That insistence is what set off the Iranian nuclear crisis. Over the years, several nations have demonstrated that it is possible to turn ostensibly civilian programs into sources of bomb fuel, and thus atomic warheads and military power. Israel recently released an archive of material, stolen from Tehran in January, to prove that the Iranian government deceived the world for years.

The Saudis, meanwhile, had no equivalent facilities. They promised to get them.

“Whatever the Iranians build, we will also build,” Prince Turki al-Faisal, a former Saudi intelligence chief, warned as the Obama administration sought to negotiate what became the 2015 nuclear agreement with Iran.

Under that pact, Iran is currently spinning a small number of nuclear centrifuges, though it had to ship 97 percent of its nuclear fuel out of the country. The Saudis believe they need to be positioned to match Iran’s every move, though experts say it would take a while. “No one thinks the Saudis would be able to do this anytime soon,” said Matthew Bunn, a nuclear expert at Harvard’s Kennedy School of Government. “They couldn’t plausibly build a weapon without outside help.”

The core challenge for the Trump administration is that it has declared that Iran can never be trusted with any weapons-making technology. Now, it must decide whether to draw the same line for the Saudis.

The United States’ own actions may be helping to drive the Saudis’ nuclear thinking. Now that the Iran agreement, brokered with world powers, is on the edge of collapse after Mr. Trump withdrew the United States, analysts are worried that the Saudis may be positioning themselves to create their own nuclear program in response.

The kingdom has extensive uranium deposits and five nuclear research centers. Analysts said Saudi Arabia’s atomic work force was steadily growing in size and sophistication — even without producing nuclear fuel.

Saudi leaders saw a political opening when Mr. Trump was elected.

In its early days, the administration spent considerable time discussing ways that Saudi Arabia and other Arab states could acquire nuclear reactors. Michael T. Flynn, who briefly served as Mr. Trump’s national security adviser, backed a plan that would have let Moscow and Washington cooperate on a deal to supply Riyadh with reactors — but not the ability to make its own atomic fuel.

As a precondition, American economic sanctions against Russia would have been dropped to allow Moscow to join the effort. Mr. Flynn was fired in early 2017 as questions swirled around his conversations with Russia’s ambassador to the United States, including about ending the trade restrictions.

In late 2017, Mr. Perry, the energy secretary, picked up the nuclear cooperation issue. Excluding Russia, he began negotiating with Riyadh over the terms. Whether the Saudis would be banned from fuel production quickly became a flash point in Congress.

At his Senate confirmation hearing in November 2017, Christopher A. Ford, the assistant secretary of state for international security and nonproliferation, called the safeguards a “desired outcome.” But he equivocated on whether the United States would insist on them.

Senator Edward J. Markey, a Massachusetts Democrat who sits on the Senate Foreign Relations Committee, described the administration’s approach as “a recipe for disaster.”

In February, Mr. Perry led a delegation to London to discuss a pact that would ban fuel production, known as a 1-2-3 agreement, for at least 10 to 15 years. (As it happens, the time frame is about how long the Iranians are banned from fuel production under the Obama-era nuclear agreement, which Mr. Trump has called “a disaster.”)

The Saudi delegation was led by the energy minister, Khalid al-Falih, who resisted the proposal.

Nuclear experts said the kingdom wanted to build as many as 16 nuclear power plants over the next 20 to 25 years at a cost of more than $80 billion. Recently, it scaled back its initial plan to the construction of just two reactors. Westinghouse, based in Pennsylvania, would provide the technology, but probably under a license to South Korean manufacturers.

The crown prince made headlines in March by shifting the public discussion over Riyadh’s intentions from reactors to atomic bombs. In a CBS News interview, he said that if Iran acquired nuclear arms, Saudi Arabia would quickly follow suit.

“Saudi Arabia does not want to acquire any nuclear bomb,” Prince Mohammed told “60 Minutes.” “But without a doubt, if Iran developed a nuclear bomb, we will follow suit as soon as possible.”

A few days later, Mr. Falih, the energy minister, raised concerns about the outcome of negotiations with Washington by insisting publicly that Riyadh would make its own atomic fuel.

He said in an interview with Reuters that he was hopeful for a deal.

“It will be natural,” he said, “for the United States to be with us and to provide us not only with technology, but to help us with the fuel cycle and the monitoring, and make sure we do it to the highest standard.”

But Mr. Falih emphasized that the kingdom had its own uranium deposits and wanted to develop them rather than relying on an overseas supplier.

“It’s not natural,” he said, “for us to bring enriched uranium from a foreign country.”

Mark Mazzetti contributed reporting from Washington, and David Kirkpatrick from London.

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