Just over four years ago, President Barack Obama used a Group of 20 summit in Pittsburgh to conduct a diplomatic ambush of Iran.

Flanked by the then leaders of Britain and France, Gordon Brown and Nicolas Sarkozy, he revealed that Iran had constructed a secret underground nuclear facility at Fordow, near the religious city of Qom. Mr Brown called it “the serial deception of many years”.

US relations with Iran may have shifted rapidly in recent weeks after 34 years of deep freeze, yet the Fordow recriminations still hang heavy over the fresh nuclear negotiations that began in Geneva on Wednesday.

The fierce political debates about the diplomatic talks with Iran have focused largely on the basic bargain at the heart of any potential deal – international sanctions relief in return for caps on Iran’s declared nuclear facilities.

But for US and other officials meeting the Iranians in Geneva, the underlying fear is that Tehran could have more secret facilities that would render any diplomatic accord meaningless.

As a result, the key part of any deal in Geneva, many officials believe, is not just about how much uranium Iran might be allowed to produce, but about the inspections that will be put in place to try to catch any covert rush to build a bomb. The details about how to monitor nuclear raw materials and production facilities for components will be crucial to any final agreement.

“We need to start with a clean slate,” said Olli Heinonen, a former senior official at the International Atomic Energy Agency, which conducts inspections of nuclear facilities.

“Iran now has industrial capacity well beyond what they had 10 years ago. And as their indigenous activity has increased, our knowledge has gone down.”

Fordow, where Iran has been enriching uranium not far short of the level needed for a bomb, was not the only nuclear facility built in secret. The other main enrichment plant at Natanz was also a covert facility at first, as was the Kalaye centrifuge research and development plant.

Some western proliferation experts believe that Iran may have other secret facilities that it has not yet declared and which, in theory, could be potentially used to produce the material for a bomb out of international inspectors’ sight.

“Suspicions are growing that Iran is building another one in secret,” David Albright, head of the Washington-based Institute for Science and International Security, told the US Senate recently. He pointed to comments in 2010 by Ali Akbar Salehi, a former Iranian nuclear neg­otiator, that studies had been done on locations for 10 other enrichment sites and that construction would shortly begin on another facility.

A dissident group, the Paris-based National Council of Resistance of Iran, said on Monday that it had un­covered evidence of another secret nuclear site, in tunnels under mountains near the town of Mobarekeh.

Iran rejected the claim as “baseless”. The NCRI did provide information that helped to uncover the Natanz facility, although some of its other claims have been debunked.

Dennis Ross, a former White House Middle East adviser, said the inspections regime would be a critical part of any deal with Iran. “We need to create circumstances where their ability to move quickly to a breakout [bomb-making] capability will be detected early on – and that they know it will be detected,” he said.

Iran did sign an “Additional Protocol” with the IAEA in 2003, which gave the agency greater inspection powers, but that agreement fell apart in 2006. Many proliferation experts believe that the IAEA, which has about 20 inspectors in Iran and visits the main sites once a week, will need authority that goes beyond the 2003 agreement.

Mr Heinonen says the IAEA does not have certain basic information about the extent of Iran’s nuclear supply infrastructure, including how much yellowcake – milled uranium – has been produced and how many centrifuges it has.

He says the IAEA will need to be able to monitor uranium mines and the mills where yellowcake is produced, as well as the factories producing the key components and machinery for the nuclear facilities – such as centrifuge rotors for enriching uranium, and the zirconium that is being used to construct a heavy water reactor at Arak.

Robert Einhorn, a former US state department official who has been involved in negotiations with Iran, says monitoring uranium mining and milling is crucial to blocking secret activity.

“Without a clandestine source of yellowcake, it would be very difficult for Iran to pursue a parallel, covert fuel cycle,” he said.

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