The International Atomic Energy Agency (IAEA) will soon remove nuclear material stored at a clandestine site in Syria after the Trump administration reached understandings with Syria and Israel, according to Israeli and US officials cited by Axios on Tuesday.
The Trump administration and IAEA scrambled to reach a diplomatic agreement to secure the material and prevent an escalation involving Israel, Syria and possibly even Türkiye over the sensitive site.
US officials said the episode validates President Donald Trump's approach to Syria and shows how the US used its close relations with the new Syrian government to neutralize a potential crisis.
The dramatic, behind-the-scenes exchange of threats and diplomacy over the secret site, which played out for months before reaching a resolution several weeks ago, was kept secret and has not been previously reported.
Assad’s nuclear program
Bashar al-Assad's regime had developed a secret nuclear program centered on the clandestine Al-Kibar reactor.
After Israel bombed the reactor in 2007, the Syrian nuclear program was mostly destroyed. But several research-and-development and storage sites remained and were mostly inactive.
After the fall of the Assad regime in December 2024, the IAEA signed an agreement with the new Syrian government that allowed it to visit the Al-Kibar reactor and several other sites connected to Syria's past nuclear activity.
Charles Lister, a resident fellow at the Middle East Institute, said Syria's new government is eager to resolve sensitive issues inherited from the Assad regime, including its nuclear and chemical weapons files, that could damage its efforts to rehabilitate the country's international standing.
One of the facilities Israel has been closely monitoring over the last two years is called “Site 99.”
According to two Israeli officials city by Axios, the Assad regime stored nuclear material there that was part of the Al-Kibar nuclear reactor project.
A US official said the material included yellowcake, a powder from uranium ore that can later be further processed and eventually enriched as part of a nuclear fuel cycle.
The US official said the regime stored other residue and “leftovers” from the al-Kibar site at Site 99.
While the material at the site can't be used for a nuclear weapon, it can be used for a “dirty bomb” - a conventional explosive device that disperses radioactive material to contaminate an area rather than produce a nuclear explosion.
The Israeli officials said the Israeli army bombed the entrances to the site shortly after the fall of the regime to prevent access to it.
For more than a year, Israel and the US have been discussing the best way to deal with Site 99, a US official told Axios.
Senior officials from the White House National Security Council and its counterpart in the Israeli prime minister's office have been working closely on the issue.
Israel made clear to the Trump administration that it would not tolerate nuclear material remaining at the site, according to an Israeli official.
Israeli officials said Israel even threatened to bomb the site again if the nuclear material was not removed or if there were signs that Syria was trying to access the material.
A US official also said that while the Israelis were concerned, they were never on the verge of bombing the site.
Cooperation with Damascus
Eventually, a US official said, the US and Israel agreed the best approach was to get a “buy in” from the Syrian government to remove the material.
When the Trump administration raised the issue with the Damascus government, Syrian officials said they didn't know there was nuclear material at the site, sources said.
“Very few people in the US, Israel and Syria were aware of this,” a US official told Axios.
The same official said the US had established a productive relationship with the post-Assad regime. “When we work with the Syrians on things — they are good partners,” the US official said.
Several weeks ago, Israelis monitoring the site detected movements in the area that led them to suspect the new Syrian government was reneging on understandings and trying to access the nuclear material, according to Israeli and US officials.
The Israelis were even concerned that Türkiye was helping the Syrian government get hold of the nuclear material.
“The Israelis are always kicking the tires on different things to make sure it looks right and it's good they do that,” a US official said.
The Trump administration asked Israel not to take any action and brought the IAEA into the picture.
The result was an agreement that was signed three weeks ago between the IAEA and the Syrian government to remove the nuclear material from the site.
The White House, the IAEA and the Israeli prime minister's office declined to comment.
US officials say the work on Site 99 is still an ongoing operation. The material hasn't been removed yet.
But “we think everybody is happy with the result. Hopefully we will be able to kick off the removal process soon and end it before the end of the year,” the official said.
