Key equipment at a sensitive Iranian military site turned out to be gone when international nuclear inspectors visited, Fox News is told, suggesting Tehran tried to “sanitize” the facility to further obfuscate how far its program had progressed, leading up to the nuclear deal.

It was only last month that the Iranians granted access to its secret military site known as Parchin.

The International Atomic Energy Agency, or IAEA, had previously confirmed that Parchin contained a so-called "containment vessel" -- a special chamber -- for testing nuclear equipment including triggers to detonate a warhead. 

Yet Fox News is told that when the IAEA toured the site for its upcoming report on Iran’s past and present program, the containment facility and equipment were gone, making it that much harder to test for radioactive residue. The source was not authorized to speak on the record.

On Sept. 21, after his visit to Tehran, the head of the IAEA, Director General Yukiya Amano, confirmed renovations had taken place at Parchin and equipment was missing but provided no further detail. 

“We entered a building which the Agency had previously only been able to observe using satellite imagery. Inside the building, we saw indications of recent renovation work. There was no equipment in the building," Amano said. 

"Our experts will now analyze this information and we will have discussions with Iran in the coming weeks, as foreseen in the Road-Map.” The “Road-Map” is shorthand for the nuclear deal agreed to by six nations, including the U.S.

“Iran needs to explain why it renovated an empty building over and over and over again,” Olli Heinonen, a ‎senior fellow at the Harvard Kennedy School of Government’s Belfer Center for Science and International Affairs, told Fox News. 

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Heinonen – who served 27 years at the IAEA and is a former deputy director – said a containment vessel can be hidden, and trace detection for radioactive material is not foolproof. “You can repaint, and pour concrete, to hide radioactive residue or simulate the tests with non-nuclear material.”    

Heinonen said the empty facility and its use must be thoroughly understood to establish what was there, and whether Teheran’s explanation makes sense and matches up with the paper trail of business records where the equipment was purchased. Tracing this back is a painstaking process, Heinonen said, much like a criminal investigation, emphasizing it would be difficult given the short timeline.

Without getting into classified information, a member of the House Intelligence Committee, who receives regular briefings, said the process is flawed.

“Now it's become clear that there was a effort to sanitize the site that went on for an extended period of time,” Rep. Mike Pompeo, R-Kan., said.

“It's likely the case that the cleanup effort may well have mitigated anything that they could have possibly have found during their inspection … As the primary guarantor of this deal, the administration has an obligation to redouble our efforts to get the surveillance and the verification right such that what the president said will be true, that the path for Iran to get a nuclear weapon were really closed.”
 
Asked Wednesday what U.S. officials knew about the equipment, the top State Department spokesman read from a statement.

“Look, for any specifics regarding the IAEA’s investigation into possible military dimensions of Iran’s program and any past concerns, I am going to refer you to the agency,” spokesman John Kirby said. 

“We have long made our assessment of Iran’s past activities and it's that assessment and the shared concerns by the international community about the nature of Iran’s past activities and Iran’s attempts to hide them that brought Iran to the negotiating table in the first place.”

The IAEA’s forthcoming report, expected in December, is important because it would pave the way for lifting the sanctions. But critics charge data is missing, and the record incomplete. On Wednesday, the IAEA offered no comment.  

A 2011 Fox News investigation called “Iran’s Nuclear Secrets”  found previous evidence of Tehran bulldozing a site of interest to inspectors, and creating an athletic field in its place.

Fox News' Pamela Browne contributed to this report.

Catherine Herridge is an award-winning Chief Intelligence correspondent for FOX News Channel (FNC) based in Washington, D.C. She covers intelligence, the Justice Department and the Department of Homeland Security. Herridge joined FNC in 1996 as a London-based correspondent.