Israel, Syria reach secret deal to remove nuclear material from hidden site

US brokers secret deal to remove nuclear material from Syrian “Site 99,” averting potential Israeli strike.

By World Israel News Staff

The US has brokered a secret agreement to remove nuclear material from a clandestine Syrian facility after Israeli intelligence detected suspicious activity around the site, defusing a crisis that officials feared could trigger a new Israeli strike and potentially draw Turkey into the confrontation.

The International Atomic Energy Agency is expected to remove the material from the facility, known as “Site 99,” under an agreement reached with the government of Syrian President Ahmed al-Sharaa about three weeks ago, Axios reported Monday, citing US and Israeli officials.

The material has not yet been extracted.

Site 99 was reportedly used by the regime of former Syrian president Bashar Assad to store material associated with its covert Al-Kibar nuclear reactor project.

Two Israeli officials said Israel has closely monitored the site for roughly two years, while a US official said the stockpile includes yellowcake — processed uranium ore that can be further refined and potentially enriched — as well as other remnants from the Al-Kibar program.

The material cannot itself be directly turned into a nuclear weapon in its current form, but officials raised concerns that radioactive material at the facility could potentially be dispersed using conventional explosives in a so-called dirty bomb.

Israel bombed the entrances to Site 99 shortly after Assad’s government collapsed in December 2024 in an effort to prevent anyone from gaining access to the material.

Israeli and US officials subsequently spent more than a year discussing how to permanently secure or remove the stockpile.

Jerusalem eventually told the Trump administration it would not accept the nuclear material remaining at the facility indefinitely and warned that the IDF could bomb Site 99 again if the material was not removed or if there were indications that Syrian forces were attempting to retrieve it.

A US official said Israel was seriously concerned about the site but was never on the immediate verge of carrying out another strike.

Washington and Jerusalem ultimately concluded that securing cooperation from Syria’s new government offered the best way to dispose of the material without risking another military confrontation.

When the Trump administration approached Damascus, Syrian officials reportedly told Washington they had not even known that nuclear material remained at Site 99.

“Very few people in the US, Israel and Syria were aware of this,” a US official said. “When we work with the Syrians on things — they are good partners.”

The issue became considerably more urgent several weeks ago, when Israeli surveillance detected movement around Site 99.

Israeli officials suspected that the new Syrian government might be backing away from earlier understandings and attempting to gain access to the stockpile.

They also became concerned that Turkey — which has developed close political and military ties with al-Sharaa’s government — could be helping Damascus reach the material.

A US official defended Israel’s scrutiny of the site, saying, “The Israelis are always kicking the tires on different things to make sure it looks right and it’s good they do that.”

Rather than allow Israel to act militarily, the Trump administration urged Jerusalem to hold off and brought the IAEA directly into the effort.

The intervention ultimately produced an agreement between Damascus and the UN nuclear watchdog roughly three weeks ago under which the IAEA will remove the material. US officials say work surrounding the facility remains underway, with the actual extraction still to come.

One US official expressed hope that the operation could be completed this year.

“We think everybody is happy with the result,” the official said, adding that Washington hopes to begin removing the material soon and finish the operation before the end of 2026.

The White House, IAEA and Israeli Prime Minister’s Office declined to publicly comment on the reported arrangement.

The episode represents the latest chapter in Syria’s long-running nuclear file.

Under Assad, Syria secretly constructed what Israel and Western intelligence agencies believed was a nuclear reactor at Al-Kibar, also known by the IAEA as Dair Alzour or Deir al-Zor.

Israel destroyed the facility in a September 2007 airstrike, an operation it did not officially acknowledge until 2018.

The IAEA concluded in 2011 that the building was “very likely” a nuclear reactor that Syria was required to declare under its safeguards obligations.

The agency’s Board of Governors subsequently found Syria in noncompliance with its nuclear safeguards agreement.

Damascus under Assad maintained that the destroyed structure had been a conventional military facility and denied nuclear cooperation with North Korea.

The dispute remained unresolved for more than a decade as the Syrian government provided only limited access to international inspectors.

That changed following Assad’s fall.

IAEA Director General Rafael Grossi met al-Sharaa in Damascus in June 2025, after which Syria agreed to cooperate with the agency with what Grossi described as full transparency and provide “immediate and unrestricted access” to sites relevant to its past nuclear activities.

The IAEA subsequently found a significant number of chemically processed natural uranium particles at one of three Syrian locations under investigation for possible links to the former Deir al-Zor program. The agency did not determine what the discovery ultimately meant, and Syria’s new authorities told inspectors they had no information explaining the material’s presence.

As recently as June, Grossi said the agency was still working with Damascus to resolve the remaining questions surrounding Syria’s former nuclear activities and that the al-Sharaa government continued to demonstrate “full cooperation.”

The deal highlights the increasingly complicated triangular relationship among Israel, Syria and Turkey.

Israel has remained deeply wary of Ankara’s expanding influence in post-Assad Syria, while Turkey has emerged as one of the strongest foreign supporters of the new government in Damascus.

According to the Axios report, US officials viewed the Site 99 episode as evidence that Washington’s engagement with al-Sharaa can provide a diplomatic mechanism for resolving security crises that might otherwise lead to Israeli military action.