The Iranian Nuclear Program and its Bureaucrat-in-Chief


During negotiations with Iran over its nuclear program, President Obama repeatedly pressed the intelligence community to make a determinative judgment on the real intentions of Ali Khamenei, Iran’s Supreme Leader. The intelligence community remained divided, however, and failed to come to a consensus on Khamenei’s policy goals.

Writing in 2009, Karim Sadjadpour of the Carnegie Endowment described Khamenei as “the single most powerful individual in a highly factionalized, autocratic regime” even though “he does not make national decisions on his own.” Instead, Sadjadpour notes, he rules “the country by consensus rather than decree, with his own survival and that of the theocratic system as his top priorities.”

Based on the few open-source documents (listed on Jeffrey Lewis’ Arms Control Wonk blog and available in FBIS) describing Iran’s nuclear decision-making after it was revealed that Iran had an undeclared nuclear program in August 2002, Iran’s nuclear policies are made by consensus and based on Khamenei’s careful bureaucratic management of Iran’s political factions. As Farzan Sahbet and this author noted, “Analyzing the Islamic Republic of Iran’s fragmented political system is a notoriously difficult task, and Tehranology is at the best of times an imprecise science.” For simplicity, Iran’s most prominent political currents are divided into four categories forming two broad camps: reformists and centrists, who together form the “moderate” camp, and neo- and traditional principalists, who constitute the “conservative” camp.

These camps were all represented in the deliberations about the direction of Iran’s nuclear policy after the National Council of Resistance of Iran (NCRI), the civilian arm of the Mujahedin Khalq (MEK), shined a light on the infrastructure supporting Iran’s two nuclear programs in August 2002. (MEK is a terrorist organization working to overthrow the Islamic Republic’s government.) The camps adopted different policies vis-à-vis engagement with the West, albeit with one key exception: all agreed on the need for Iran to maintain its enrichment program, and thereby ensure that its “right to enrich” was not undermined. Iran’s subsequent decision-making reflected the country’s politics. During times of conservative empowerment (2005-2013), Iran grew more combative. By contrast, during times of “moderate” rule (1998-2005; 2013-Present), Iran was more amenable to political compromise on the nuclear issue.

In the latest round of negotiations, Iran’s moderates have the upper hand, which suggests that the United States has an overarching interest in pushing forward with negotiations intended to reach a final agreement to the dispute over Iran’s nuclear program. The current Iranian government is moderate in its outlook, which means that the international community has an opportunity to finalize an agreement with robust inspections. A more conservative government, for example, may balk at the terms required to assure the world that Iran’s nuclear program is peaceful.

Moreover, Iran’s commitments – released in a U.S. government fact sheet about the negotiations – further suggest that key Iranian moderates are influencing nuclear decisions and, most importantly, have been able to sway the Supreme Leader to tepidly embrace their positions. Iran has made key concessions that if implemented will severely curtail any conceivable route to the bomb. This position is at odds with Khamenei’s history of support for Iran’s nuclear weapons program, as well as the policies pursued by conservative elements between 2005 and 2013. However, they are in line with Iran’s diplomatic history, suggesting that the route to a successful negotiation started in Tehran.

The Nuclear Program

Iran’s nuclear weapons program began in 1985. Two years later, Khamenei personally led a delegation to Pakistan to procure the front-end of the nuclear fuel cycle. A year after, a representative from Iran’s Revolutionary Guards Corp met with a representative from the AQ Khan network in Dubai. Iran ultimately purchased the list of Khan’s European suppliers for specialized centrifuge components, as well as a document detailing the reduction of uranium gas to metal and then the manufacturing of the precise spheres used in the core of a nuclear weapon.

Iran subsequently divided its nuclear program into two. The Atomic Energy Organization of Iran (AEOI) oversaw the civil side of the program and was based at Tehran University and later at the Kalaye Electric facility, where Iran first enriched uranium in 1999. The military’s efforts were separate from the AEOI’s work, and further divided into two components: the first centered on procurement and was based at Sharif University; and the second focused on developing the tools and designs needed to deliver and detonate a nuclear warhead. This program, it appears, was based at Lavizan Shian.

Bureaucratic Politics

After the NCRI revealed much of Iran’s undeclared nuclear infrastructure in August 2002, Khamenei put together a bureaucratic entity dubbed the “Council of Heads” to craft and review Iran’s nuclear policies, particularly as they pertained to the then negotiations with the EU-3. The Council was under the direction of Hassan Rouhani, but included key conservative leaders like Minister Ali Akbar Velayati and the Khamenei-appointed director of the AEOI, Gholam Reza Aghazadeh. This entity balanced the interests of the so-called conservatives and moderates, which thus gives Iranian nuclear researchers a glimpse into the inter-bureaucratic dynamics underpinning the Iranian nuclear negotiating position.

During these debates, Khamenei acted as the bureaucrat-in-chief, and ultimately sought to balance the conflicting proposals put forward by Iran’s differing political factions. From the outset, the moderate camp advocated for a more conciliatory approach to the West, whereas Aghazadeh and Velayati both argued in favor of a more hardline approach. The AEOI’s position, it appears, was based on ignorance and a lack of understanding about the IAEA’s environmental sampling techniques used to detect particles of enriched uranium.

According to Rouhani, the AEOI was “taken aback” by the results of IAEA sampling, before learning that contamination came from the centrifuges purchased from Pakistan. These surprises, in turn, resulted in Rouhani working to bring “all issues involving the nuclear case … under one person’s authority” and his “orders be mandatory for all organizations related to the case.” Having learned this lesson, it stands to reason that the IAEA now serves as a deterrent against Iranian cheating at declared facilities – with the contamination at Sharif University remaining a point of suspicion about a potential military program.

The Foreign Ministry, by contrast, was concerned about the possibility of Iran’s nuclear case being referred to the United Nations Security Council, which would imply indirectly the potential for U.S.-led military action. This debate was taking place months after the United States and its coalition partners easily defeated the Iraqi military during its march to Baghdad, and before the start of the insurgency. Indeed, the United States was at the apex of its power in the region, and thus the speculation that Iran could be next was rife in Western and regional capitals.

Despite this threat, Iran still sought to find a middle ground. The Council never endorsed a plan to end enrichment. Instead, the policy was to pursue a strategy of “suspension,” whereby Iran would retain its nuclear infrastructure after the questions about its nuclear program were resolved. This suggests that threat of U.S. military action, while a salient factor in these early negotiations, was second to that of Iran’s steadfast insistence on maintaining some semblance of an enrichment program.

This position was ultimately reflected in the language in the 2004 Paris Agreement, which entailed Iran “suspending” enrichment and conversion, but not an Iranian commitment to give up its enrichment program. Khamenei’s actions during this period suggest that he was the final arbiter on Iran’s nuclear policy. However, that policy was shaped during debates in the Council of Heads. Between 2003 and 2005, Khamenei sought to balance the moderate and conservatives factions’ against one another and ultimately endorsed a middle ground, whereby he agreed to suspend enrichment and conversion, albeit while keeping elements of the military program in place.

Khamenei’s deference to the moderate position shifted in 2004, owing to the empowerment of the Iranian conservative movement, and the eventual election of hardliner Mahmoud Ahmadinejad. Thereafter, Iran’s position began to reflect the more conservative members on the Council of Heads; ultimately resulting in Iran restarting its enrichment program in 2006. This policy shift took place at a time when the U.S. military option had not yet been discredited. This suggests that domestic politics drive Iran’s decision-making calculus – and therefore Iran’s willingness to cooperate after the 2013 election of Rouhani is indicative of the empowerment of Iran’s moderates over that of the conservative movement.

The Return of the Moderates

The United States was caught off-guard when Hassan Rouhani beat the Khamenei-favored Mohammad Bagher Ghalibaf in the 2013 election. During the campaign, Iran’s moderates endorsed reaching a nuclear agreement with the P5+1. Following Rouhani’s victory, Khamenei authorized the negotiations by calling for “heroic flexibility” and labeling Javad Zarif, Iran’s Foreign Minister, and his negotiating team as “children of the Revolution.” Iran’s position during the recent multi-staged negotiations was similar to that of its position in 2003. Enrichment remained the one red line, but in a similar position to that of the Foreign Ministry between 2003 and 2005, the Iranian side was far more willing to make serious concessions.

There are three key differences from Iran’s previous moderate-led negotiations. First, as of 2014, Iran had installed some 19,000 centrifuges under vacuum of which about 10,000 were actually enriching uranium. Second, during the Ahmadinejad presidency, Iran decided to build a secret centrifuge facility, near the city of Qom. The facility is buried under a mountain and is impervious to all but the latest version of U.S. penetrating munitions. Third, within the latest iteration of Iran’s internal bureaucratic debates, the 2003 Khatami position favoring greater transparency appears to have won out.

Balanced against these key challenges has been the centralization of Iran’s nuclear file. Rouhani, speaking in 2005, notes that before the revelation in August 2002 that the program was fragmented and few people inside Iran had a complete understanding of Iran’s nuclear research. This admission further suggests that there was, in fact, two centrifuge programs in Iran. Centralization, in turn, has streamlined Iran’s negotiating position and may explain why the position long-held by Iran’s moderates were reflected in the U.S. fact sheet.

The Agreement and the Challenges

These political changes – and the proposed policy fixes – are evident in the U.S. drafted fact sheet on the parameters of the final agreement the two parties will try to reach before the end of June. Iran has agreed to reduce the number of centrifuges installed at Natanz to ensure that the time needed to enrich a reduced stockpile of low enriched uranium to 90% would be greater than or equal to one year. To do so, Iran will decrease the number of centrifuges installed at Natanz to 5,104. The key P5+1 concession, it appears, is the allowance of 1,000 centrifuges at Fordow, while requiring Iran to remove fissile material from the site and mandating that the installed centrifuges don’t spin uranium hexafluoride gas – and thus will not be producing enriched uranium at the site.

Instead, per Zarif’s comments on the subject, the facility will be upgraded with an unnamed P5+1 member state to produce medical isotopes, which probably entails only a select number of the 1,000 centrifuges on site separating non-fissile isotopes for medical purposes. Similarly, the U.S. fact sheet indicates the core of Iran’s heavy water reactor, the IR-40, will be replaced to decrease the amount of plutonium produced from the fuel rods. Moreover, in a concession that the United States has been trying to wrangle from Iran for close to five decades, the agreed framework includes an Iranian agreement to forego reprocessing.

To further protect against the threat of Iranian “sneak-out,” whereby Iran could try and construct a secret facility to enrich uranium, the U.S. fact sheet calls for inspections in centrifuge machine shops and, critically, the monitoring of Iran’s uranium mines and uranium conversion facility. These twin provisions, once enforced, will allow for the IAEA to monitor the complete front-end of Iran’s nuclear fuel cycle – and thereby ensure with a level of credibility that Iran cannot produce centrifuges in secret, syphon off uranium converted at the conversion facility, and then enrich it in an undisclosed location. These inspections, when paired with the conversion of Arak and the agreement not to reprocess, deprive Iran of any conceivable route to acquiring the necessary fissile material (enrich uranium or separated plutonium) to construct a nuclear weapon.

The potential problems stem from the pace and sequencing of sanctions relief, which appears tied to Iran’s on-going discussions with the International Atomic Energy Agency about the allegations surrounding its previous weapons-related experiments. The sequencing and pace of sanctions relief remains the biggest obstacle to the drafting of a final accord. The two sides have never been closer to signing a comprehensive agreement that would address the international community’s justifiable concerns about Iran’s nuclear program. The framework – should it be finalized – is robust and includes hitherto never implemented inspection provisions to ensure that Iran cannot cheat and surreptitiously develop nuclear weapons.

The available evidence indicates that Khamenei remains Iran’s bureaucrat-in-chief and is taking his cues from the moderates beneath him. Enrichment remains a key red line, but at least for now the faction within Iran advocating for greater transparency has the political weight within the bureaucracy to conclude an agreement with robust nonproliferation provisions. The critical test is still to come. Iran still has to finalize the agreed upon framework. There is little doubt that the sanctions issue will remain difficult to overcome. But there is indication that both sides have sufficient political will to overcome this decades old problem. This political will, in turn, stems from the empowerment of Iranian moderates, who have long advocated for an agreement with P5+1, but lacked the bureaucratic influence to convince the Supreme Leader.


Aaron Stein is a doctoral fellow at the Geneva Center for Security Policy and an associate fellow at the Royal United Services Institute in London.