Ayatollah Mojtaba Khamenei's order could further frustrate US President Donald Trump and complicate talks on ending the US-Israeli war on Iran.
Israeli officials have told Reuters that Trump has assured Israel that Iran's stockpile of highly enriched uranium, needed to make an atomic weapon, will be sent out of Iran and that any peace deal must include a clause on this.
Israeli Prime Minister Benjamin Netanyahu has said he will not consider the war over until enriched uranium is removed from Iran, Tehran ends its support for proxy militias, and its ballistic missile capabilities are eliminated.
"The Supreme Leader’s directive, and the consensus within the establishment, is that the stockpile of enriched uranium should not leave the country,” said one of the two Iranian sources, who spoke on condition of anonymity because of the sensitivity of the matter.
Iran's top officials, the sources said, believe that sending the material abroad would leave the country more vulnerable to future attacks by the United States and Israel. Khamenei has the last say on the most important state matters.
The White House and Iran's foreign ministry did not respond to requests for comment.
Deep suspicion among top Iranian officials
A shaky ceasefire is in place in the war that began with US-Israeli strikes on Iran on February 28, after which Iran fired at Gulf states hosting US military bases and fighting broke out between Israel and Hezbollah in Lebanon.
But there has been no big breakthrough in peace efforts, with a US blockade of Iranian ports and Tehran's grip on the Strait of Hormuz, a vital global oil supply route, complicating negotiations mediated by Pakistan.
The two senior Iranian sources said there was deep suspicion in Iran that the pause in hostilities was a tactical deception by Washington to create a sense of security before it renews airstrikes.
Iran's top peace negotiator, Mohammad Baqer Qalibaf, said on Wednesday that "obvious and hidden moves by the enemy" showed the Americans were preparing new attacks.
Trump said on Wednesday the US was ready to proceed with further attacks on Tehran if Iran did not agree to a peace deal, but suggested Washington could wait a few days to "get the right answers."
The two sides have started to narrow some gaps, the sources said, but deeper splits remain over Tehran's nuclear programme — including the fate of its enriched uranium stockpiles and Tehran's demand for recognition of its right to enrichment.
Iran hardens stance on enriched uranium stockpile
Iranian officials have repeatedly said Tehran’s priority is to secure a permanent end to the war and credible guarantees that the US and Israel will not launch further attacks.
Only after such assurances are in place, they said, would Iran be prepared to engage in detailed negotiations over its nuclear programme. Tehran has long denied seeking a nuclear bomb.
Israel is widely believed to have an atomic arsenal but has never confirmed or denied it has nuclear weapons, maintaining a so-called policy of ambiguity on the issue for decades.
Before the war, Iran signalled willingness to ship out half of its stockpile of uranium, which has been enriched to 60%, a level far higher than what is needed for civilian uses.
But sources said that the position changed after repeated threats from Trump to strike Iran.
Israeli officials have told Reuters it is still unclear whether Trump will decide to attack and whether he would give Israel a green light to resume operations. Tehran has vowed a crushing response if attacked.
However, the source said there were "feasible formulas" to resolve the matter.
"There are solutions like diluting the stockpile under the supervision of the International Atomic Energy Agency," one of the Iranian sources said.
The IAEA estimates that Iran had 440.9kg of uranium enriched to 60% when Israel and the US attacked Iranian nuclear facilities in June 2025. How much of that has survived is unclear.
IAEA chief Rafael Grossi said in March that what remained of that stock was “mainly” stored in a tunnel complex in its Isfahan nuclear facility, and that his agency believed slightly more than 200 kg of it was there. The IAEA also believes some is at the sprawling nuclear complex at Natanz, where Iran had two enrichment plants.
Iran says some highly enriched uranium is needed for medical purposes and for a research reactor in Tehran which runs on relatively small amounts of uranium enriched to around 20%.
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