In February 2004, senior IAEA officials led by Director General Mohamed ElBaradei held a one-off meeting in Tehran with former President and parliamentarian Akbar Hashemi Rafsanjani. Based on an assessment of Iran’s nuclear program which the IAEA is currently preparing for the Board of Governors, after that report is completed it might be appropriate at some point for Director General Yukiya Amano to request a second meeting.

Since 2004, the IAEA has obtained a lot of information documenting that military-linked research and procurement organizations were involved in Iran’s nuclear program. Some of that activity was carried out during the presidency of Seyed Mohammad Khatami, from 1997 through 2005. Some individuals the IAEA have identified as having been engaged in this activity were also in the program under Rafsanjani’s presidency, from 1989 through 1997.
ElBaradei met Rafsanjani before the IAEA started compiling that dossier on weapons-related activities. At that time, the IAEA had much broader issues on its plate with Iran, including a discussion of implementation of the Additional Protocol by Iran. The meeting with Rafsanjani was squeezed into a packed itinerary included meetings between ElBaradei and other Iranian political luminaries, including President Khatami, Foreign Minister Kamal Kharrazi and the Speaker of Iran’s Parliament, Hojjatoleslam Mehdi Karroubi. Diplomacy, courtesy, and confidence-building were the watchwords for these meetings.
Nonetheless, the IAEA’s meeting with Rafsanjani had an extraordinary moment: During the discussion, Rafsanjani at one point became very emotional and nearly broke into tears when he described having witnessed the results of a battlefield poison gas attack on Iranian front soldiers during Iran’s eight-year war with Iraq, ordered by Saddam Hussein. Rafsanjani had described a state of affairs during that war when, after the poison gas attack, and the virtual absent response to it by the rest of the world, as one participant in IAEA-Iran diplomacy related, the very existence of the Iranian state was at stake.
The IAEA never sat down with Rafsanjani again.
About a year later, the IAEA began obtaining an increasing stream of evidence suggesting there is a “possible military dimension” (PMD) in Iran’s nuclear program, and that Iran had taken steps, in procurement and in conducting R&D activities, which would be useful for developing nuclear weapons. The IAEA’s dossier on these activities after 2005 continued to grow–it contains historical information on HE testing, firing systems, neutron research, a nuclear-capable missile reentry vehicle, chemical processing of uranium to metal, procurement of high-speed cameras–which suggests a composite picture of dedicated Iranian interest in this subject. By 2008, the IAEA had been routinely investigating Iran’s program for six years, and the IAEA’s files on Iran’s nuclear program were comprehensive enough for the agency to ask Rafsanjani some questions about nuclear decision making and about what he knew was going on in the nuclear program. Rafsanjani answered these questions, but the IAEA was not satisfied with all of the answers he provided.
As I suggested here way back in June, the IAEA will very shortly provide an assessment of Iran’s nuclear program including its military dimension to the Board of Governors. We hear that an initial version of the report, for Amano, has been drafted and that it is now being amended.
The current mantra from Iran on this is that all the information on PMD in the IAEA’s files is falsified. That wasn’t the Iranian view in the past, as late as 2008, however, because Iran knew that the IAEA had multiple sources for this information. Until around 2008 there was no Iranian idee fixe that the Department of Safeguards was spoon-fed all this stuff by the US and Israel and other governments hostile to Iran, and that the rest of it came from unqualified open-source references. Iran was prepared in fact to discuss some of the information then because it knew that at least some of the IAEA’s information was genuine. But those were different times.

Who decided?

There is some continuity in the IAEA’s composite Iran picture, permitting the agency to establish that certain individuals with links to military-related organizations in Iran appear to have been consistently involved in weaponization-related R&D and procurement activities. 
But it is far less clear who key personel in Iran–including Mohsen Fakhrizadeh, a leading scientist–are taking orders from. And it would appear that difficulties experienced by the IAEA in assigning personal responsibility or authority for directing nuclear activities in Iran involving military-affiliated personnel and organizations–in particular the Iran Revolutionary Guard Corps (IRGC)–may be similar to problems the U.S. government is currently facing in trying to establish a watertight connection between suspects it says were planning to assassinate the Saudi ambassador in Washington, and higher-ups at the top of the Iranian government.
The line we heard from the U.S. last week that there was a direct connection between the alleged perpetrators of the foiled assassination plot and Iran’s top leadership has since been qualified by some U.S. officials who acknowledge that that relationship might not be so direct after all. In the IAEA’s nuclear investigation, similar forensic problems have arisen over the last five or six years.
If there is a smoking gun in the US government case against Iran’s leadership in the foiled assassination plot allegations this week, it’s that someone in Iran was prepared to wire across USD 100,000 to pay for services rendered. In the nuclear investigation, the IAEA has some information showing that money was allocated for activities which appear to be military-related in Iran. But there’s no slam-dunk record on file showing that someone at the top of the Iranian regime authorized scientists or procurement agents to go for broke and steer the nuclear program in the direction of nuclear weapons.
The Iranians have been masters in compartmentalizing their nuclear program. Some scientists who have been doing research that looks like it may be related to nuclear weapons development aren’t even aware that they are part of the nuclear program. But it would be a mistake to assume that decisions about these activities are not being made at a very high level.
Was Rafsanjani ever a decision maker in this area? I have no idea. Some people in the VIC over the last couple of years have asked that question, going back to that Tehran meeting with ElBaradei when Rafsanjani related his reaction to those Iraqi poison gas attacks.
Before he was elected President of Iran Rafsanjani had a senior military role during the Iran-Iraq war. If this report is to be believed, in 1988, a year before his election as President, Rafsanjani was appointed by the Ayatollah Khomenei as head of Iran’s armed forces, and that during his tenure he advanced control over the military by the IRGC–a military organization which U.S. officials have asserted again and again since the 1990s was responsible for key parts of Iran’s nuclear program (and is at the center of U.S. assassination allegations now) . But the report also suggests that pro-Rafsanjani personalities in the IRGC were removed after Rafsanjani became President of Iran. During Rafsanjani’s presidency, however, the weight and power of the IRGC in Iranian politics and the economy considerably magnified.
The first Iraqi chemical weapons attack on Iran was in 1983. My understanding is this: Iraqi chemical attacks provoked Iran to mull how to most effectively respond to such an attack in the future. The world was virtually silent when those attacks on Iran were carried out. It would be logical that decision making on Iran’s response would involve the country’s top leadership as well as its military. Decisions were taken–somewhere, by someone–to do nuclear military-related R&D work in specific areas sometime after the Iraqi chemical attacks were carried out. 
Rafsanjani has been named as a top-level actor in highly-sensitive decision making before, outside the nuclear realm, involving terrorist attacks on foreign soil which governments say were piloted by Iran. But to my knowledge, these allegations haven’t been substantiated or have been disputed. One such case was in Argentina, where a prosecutor asserted that Rafsanjani was co-responsible for a 1994 attack on on a Jewish organization in Buenos Aires. The prosecutor failed however to make those charges stick in Interpol arrest warrants. In another case, in Germany in 1992, prosecutors charged that Iran’s intelligence chief, Ali Fallahian, masterminded a deadly attack on Kurdish opposition figures in a restaurant in Berlin. They also asserted that Rafsanjani was implicated but some of the testimony from at least one witness who linked Rafsanjani to the attack was based on assumptions, not hard evidence.
Would Rafsanjani be in the position to help the IAEA better understand what’s in that assessment we will likely read in a few weeks? The IAEA might find the man at times described as Iran’s ultimate political survivor difficult to pin down, but he’s no longer in power, and I would hazard the guess that, if he is highly confident that Iran’s uranium enrichment program will survive, Iran’s ex-President might now have some illuminating answers to questions the IAEA first asked him three years before.