Iranian President Hassan Rouhani welcomes Yukiya Amano, the head of the IAEA, in Tehran, Iran, on September 20.Ebrahim Noroozi / AP

The head of the U.N. nuclear-watchdog agency says his visit over the weekend to Iran’s Parchin military site is “significant progress” in the organization’s investigation of the Islamic Republic’s nuclear activities.  But Yukiya Amano, who heads the International Atomic Energy Agency, also noted that environmental samples taken at Parchin were collected by Iranian officials before the IAEA’s visit.

Here are Amano’s comments on his visit—the first time the IAEA has been allowed access to the facility:

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. Our experts will now analyse this information and we will have discussions with Iran in the coming weeks, as foreseen in the Road-map.

As I have stated in my reports to the Board, the extensive work that has been conducted at the location since early 2012 undermines the Agency’s ability to conduct effective verification there.  

Before our visit, certain IAEA safeguards activities were carried out at the particular location at the Parchin site. These included the taking of environmental samples.

Sample taking is a complex process.

As a result of experience gained over the years, the Agency has, in certain circumstances, permitted States’ representatives to carry out activities in support of the Agency’s verification work. This is done in a way that ensures that the Agency’s verification processes are not compromised.

In the case of Parchin, the Iranian side played a part in the sample-taking process by swiping samples.

The Agency can confirm the integrity of the sampling process and the authenticity of the samples, which were taken at places of interest to the Agency at the particular location in Parchin.

Authentication by the Agency of the samples was achieved through use of an established verification process. The process was carried out under our responsibility and monitoring. The samples have been brought to Vienna and will be analysed by Agency experts.

Amano’s assurances notwithstanding, the collection of samples by the Iranians is unlikely to assuage concerns about the nature of the deal struck between Iran and the U.S. and other world powers over the Islamic Republic’s nuclear program. Here’s Reuters:

The IAEA has come under criticism over a confidential agreement with Iran governing how inspections are conducted at Parchin. Critics of the big powers’ deal with Iran have argued that the IAEA’s approach limits its ability to investigate and gives Iran too much influence in the collection of samples.

Under that arrangement, the samples would be taken by Iranian technicians while IAEA experts present at Parchin would observe and oversee the process, Western diplomats told Reuters.

Reuters also reported that Behruz Kamalvandi, a spokesman for the Atomic Energy Organization of Iran, told an Iranian news agency that the samples taken this week at Parchin were given to the IAEA’s experts.

“He did not rule out IAEA inspectors being present for future samples being taken,” Reuters added.

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