Iran’s Supreme Leader, Ayatollah Ali Hosseini Khamenei, is the most important player in decisions on Iran’s nuclear program. For anything that Iran’s new president-elect, Hassan Rouhani, may propose to the outside world to solve the Iranian nuclear crisis, we won’t know for a fact whether Rouhani will be acting upon specific instructions from Khamenei. But we do know that any nuclear initiative sponsored by Rouhani will have the endorsement of the Supreme Leader. So in the aftermath of Rouhani’s election, we had better pay close attention to what Khamenei says.

Including this item from last week, for example:

In regard to the International Atomic Energy Agency, Khamenei said, “The agency has acknowledged that the problems it has had with Iran’s nuclear program have been resolved; therefore, Iran’s nuclear case should be closed.”

Iranian officials have frequently employed language like this to urge the IAEA to terminate its ten-year investigation of Iran’s nuclear history and activities and return to what Iran calls “routine safeguards.” But on this point, the Supreme Leader has been misinformed.

The IAEA has not “acknowledged that the problems it has had with Iran’s nuclear program have been resolved.”

The IAEA Board of Governors, from its first Iran resolution in September 2003 has called on Iran to cooperate fully with IAEA to ensure verification of compliance with Iran’s safeguards agreement [operative paragraph 4] and requested Iran to fully implement its Additional Protocol [operative paragraph 6]. As the IAEA has investigated Iran’s nuclear program at the behest of the IAEA Board of Governors since 2003, some issues included in the Agreed Workplan of August 2007 have been understood well enough for IAEA to say they were “not outstanding at this stage” of their investigation, but not resolved. These issues included contamination on P1 and P2 centrifuges, polonium-210, and the Gchine uranium mine.  The IAEA resolved questions about Iran’s plutonium experiments. But the key issue – possible military dimensions to Iran’s nuclear activities – has not been resolved.

The IAEA has a list of questions it wants answers to from Iran. What’s on the list? We don’t exactly know since the IAEA has not made public its compendium of questions. Based on what the IAEA has told its Board of Governors over time, we can assume that there are outstanding questions about “alleged studies” on UF4/”green salt” production, high-explosives testing, and missile re-entry vehicle projects [GOV/2008/4 paragraph 35]; acquisition of uranium metal [paragraph 19] R&D activities of military-related institutes and companies that could be nuclear-related [paragraph 40-41]; and about production of components by companies owned by Iran’s national defense industry [GOV/2004/11 paragraph 37 and GOV/2004/34 paragraph 22]. These issues cited here were included in IAEA reports from the period 2003-2008. They and additional questions concerning the “possible military dimension” of Iran’s nuclear program were elaborated by the IAEA in a report to the board in November 2011. The IAEA is also interested in pyroprocessing, irradiation of uranium targets, and recovery of uranium from ash.

States with Additional Protocol

For a state that has an Additional Protocol in force, after the state provides a so-called initial expanded declaration of its nuclear-related activities, questions and inconsistencies would be evaluated by the IAEA in consultation with the state.

The IAEA began implementing the Additional Protocol in states with comprehensive safeguards agreements (CSA) soon after approval by the IAEA Board of Governors in 1997. Since then the record shows that doing the evaluation can take many years for countries like Iran with complex nuclear programs including R&D and fuel processing installations.

At the end of this process, the IAEA reaches a so-called “broader conclusion” which is defined by the IAEA Safeguards Glossary as follows:

For each State with a CSA and an additional protocol based on [Infcirc/540] in force, a broader conclusion can be drawn for the year concerned that all of the nuclear material in the State had been placed under safeguards and remained in peaceful nuclear activities or was otherwise adequately accounted for. To be able to draw this conclusion, the IAEA must draw the conclusions of both the non-diversion of the nuclear material placed under safeguards and the absence of undeclared nuclear material and activities for the State as a whole. The conclusion of the absence of undeclared nuclear material and activities is drawn when the activities performed under an additional protocol have been completed, when relevant questions and inconsistencies have been addressed, and when no indications have been found by the IAEA that, in its judgment, would constitute a safeguards concern.

The broader conclusion for each state is reviewed annually. For 2012, the IAEA provided the broader conclusion for 60 of the 114 states that have both a CSA and an AP. For the other 54 states with CSA/AP, in 2012 the IAEA found “no diversion of declared nuclear material from peaceful nuclear activities.” Because verification in these states was incomplete by the end of 2012, however, the IAEA told the board last month that “evaluations regarding the absence of undeclared nuclear material and activities remained ongoing.”

AP and Iran

What’s all this got to do with Iran?

In December 2003, Iran and the IAEA signed an Additional Protocol for Iran, and in May 2004, Iran submitted an initial expanded declaration to the IAEA. Iran however never ratified the Additional Protocol and has suspended its implementation since 2006.

Given Iran’s past track record of systematic omissions and failure to declare nuclear activities to the IAEA, the international community wants Iran to ratify and implement its Additional Protocol to provide confidence that all of Iran’s nuclear activities are dedicated to peaceful use. In return, successful implementation of the Protocol should mean that over time the IAEA’s verification of Iran’s nuclear program would gradually be reduced to the level of other states that have CSAs and APs in force and similar nuclear programs.

Moving forward with Rouhani means making progress on two tracks–the political track and the IAEA track.

The political track requires negotiation of a political agreement between Iran and the powers—this should be in parallel with U.S. bilateral discussions with Iran— which should include agreement about what nuclear activities Iran will do and what other activities Iran agrees not to do. The agreement may include incentives provided to Iran (such as these incentives for future nuclear cooperation) and a confidence-building verification protocol; it will have to resolve how the United Nations Security Council’s demand for suspension of all Iranian enrichment-related and reprocessing activities will be handled; and, last but not least, it must incorporate a robust verification mandate for the IAEA in Iran. In practice such a political agreement will depend on Iran’s political will, bolstered by incentives in the deal Iran makes with the powers.

How could IAEA verification go forward under such an agreement?  One roadmap to resolution looks something like this:


  • Iran voluntarily brings into force its Additional Protocol, and submits an updated expanded declaration to the IAEA, including information on unreported activities prior to 2003;


  • In parallel, Iran voluntarily adopts the modified Code 3.1 of its Subsidiary Arrangements General Part on early design information and submits declarations under it to the IAEA on new reactors and enrichment facilities, as well as on the IR-40 heavy water reactor at Arak;


  • The IAEA, after receiving the expanded declaration for the Additional Protocol submitted by Iran, begins the process that can lead to a broader conclusion, with the recognition by Iran that getting to the broader conclusion will take a long period of time;


  • The IAEA will consider issues related to the “possible military dimensions” of Iran’s nuclear program prior to 2003 (including access to the Parchin site) as part of the evaluation of Iran’s AP expanded declaration. These issues may not be resolved quickly but they would have to be resolved prior to the IAEA giving Iran a broader conclusion.


It would be fair to say that for a few states with complex nuclear fuel cycle programs, some issues have been evaluated by the IAEA during implementation of the Additional Protocol whose resolution required about five years. In the case of Iran, given that the IAEA has since 2003 learned quite a bit about Iran’s nuclear program, it might be possible to arrive at a broader conclusion in two to three years—provided that Iran fully cooperates with the IAEA.

The IAEA does not “close files.” Terms of its safeguards agreements and Additional Protocols obligate the IAEA to perform ongoing evaluation that all nuclear material remains in peaceful activities. This may include requests for access to locations and information on the basis of new information raising questions about the correctness and completeness of the state’s declarations.

As Iran implements the above steps, and the international community develops growing confidence in the fully peaceful nature of Iran’s nuclear activities, the intensity of IAEA safeguards implementation on declared nuclear material in Iran will come into accordance with the practice in other NPT states which have an Additional Protocol. That assumes however that Iran’s leaders’ repeated statements that Iran is only interested in peaceful uses of nuclear energy are true.