Before Ayatollah Ali Khamenei became Iran’s supreme leader in 1989, he was a member of Ayatollah Ruhollah Khomeini’s inner circle. But when Khomeini, founder of the Islamic Republic, was alive, Khamenei also made news by challenging his wishes from time to time. On one such occasion, which overshadowed all others, Khamenei, then president, opposed Khomeini’s support for then-Prime Minister Mir Hossein Mousavi. The controversy lasted from August to October 1985, and became the biggest political crisis in the Islamic Republic since the ousting of Iran’s first post-revolutionary president, Abolhassan Banisadr, in 1981.

The crisis between Khamenei and Mousavi began that same year when Khamenei became president about four months after Banisadr was removed. At that time, the constitution provided for both a president and a prime minister, and Iran’s parliament leaned towards choosing Mousavi as Prime Minister. Khamenei, unhappy with the choice, did his best to deny Mousavi the office. He first nominated Foreign Minister Ali Akbar Velayati, but Velayati failed to get a vote of confidence. Khamenei then floated the names of his allies Ali Akbar Parvaresh and Mohammad Gharazi, but parliament let him know that they had no chance. Khamenei was then forced to nominate Mousavi, who received a vote of confidence on October 31, 1981.

The Battle Is Joined

In 1985, Khamenei was reelected president and was determined to end Mousavi’s premiership at any price. But he failed to foresee that Khomeini would offer Mousavi his staunch support.

In his diary from the period, Akbar Hashemi Rafsanjani, one of the founding figures of the Islamic Republic, who was then speaker of parliament, has described the crisis. On August 6, 1985, Rafsanjani met Khamenei to discuss the matter. They decided to put the question to Ayatollah Khomeini. Two days later, Khamenei reported that Khomeini had rejected his wish to end Mousavi’s premiership.

On August 11, Rafsanjani wrote that Khamenei was asking him for help. “He expects me to facilitate his efforts to change the cabinet,” Rafsanjani wrote. “He suggests that the Imam [Khomeini] must somehow change his view about the prudence of Mousavi remaining in office, but I think it is unlikely that the Imam would do so.

On August 12, another meeting took place. This time, Khomeini’s son Ahmad was also present, and he reiterated that Khomeini believed Mousavi’s removal would be imprudent.

Now that Khomeini had rejected Khamenei’s wishes, Khamenei decided to assert his role in choosing a prime minister by issuing a formal statement. “Only if the Imam orders it will I appoint him,” he said of Mousavi. “In this case, I would not interfere in any way and Mr. Mousavi can choose all the cabinet ministers as he wishes.”

“We are going to have a big problem”

Rafsanjani was getting worried about Khamenei’s persistence. “We are going to have a big problem,” he wrote in his diary.

Ali Akbar Nateq-Nouri, Iran’s interior minister at the time, agreed with Khamenei. Khamenei, Nateq-Nouri wrote in his diary, “wrote a letter to the Imam saying, ‘If your Excellency is of the opinion that I must nominate Mr. Mousavi, then order me to. You are the leader and on Judgement Day you have the answer, but I cannot justify appointing somebody to the premiership whom I do not find prudent, unless he is supported by the Imam’s mandate.’ But the Imam said, ‘I am not giving an order. I am only saying what I have to say.’ It was a strange deadlock.”

According to Rafsanjani’s diary, on August 14, Khomeini held a meeting, which Khamenei avoided. “We were the guests of Master Ahmad [Khomeini] for dinner,” Rafsanjani wrote. “The Imam was present, too. Mr. Khamenei was absent because his parents were visiting. Most of the discussions revolved around the next prime minister and the disagreements between Messrs. Khamenei and Mousavi. But nothing was settled.”

In Khamenei’s absence, Rafsanjani had to mediate. Khomeini was not willing to compromise with Khamenei. “I went to the Imam and talked with him about the problem of the next cabinet and the opposition of Mr. Khamenei to Mr. Mousavi,” Rafsanjani wrote in a diary entry dated August 24. “There was no resolution. The Imam repeated that he did not consider it prudent to change the cabinet, that he would not issue a decree, and that his expressed opinion was sufficient.”

Khomeini rejects a face-saving solution

To save Khamenei embarrassment, Rafsanjani suggested that Khomeini should advise the Guardian Council to reinterpret the constitution in such a way that when a new president was inaugurated, there would be no need to change the cabinet. This way, Mousavi could continue as prime minister without Khamenei having to reappoint him. But Khomeini rejected this. “I said there would be trouble,” Rafsanjani wrote, noting that Khomeini “told me to talk to Mr. Khamenei and convince him. He said that this would hurt Mr. Khamenei himself.”

Following Khomeini’s remark, Foreign Minister Velayati, whom Khamenei had hoped to nominate for the premiership, got cold feet. On September 2, Rafsanjani wrote, “Considering the statements by the Imam saying that removing Mr. Mousavi is not prudent, the foreign minister asked me to tell Ayatollah Khamenei not to mention his name as a candidate.”

The Whining Inauguration

Khamenei, however, was not ready to defer to Khomeini. Even during the inauguration ceremony, Khamenei indirectly criticized Mousavi in front of Khomeini. Afterward, Khamenei hoped to enlist Rafsanjani’s help, and repeatedly visited his office. “Mr. President was here,” Rafsanjani wrote on September 7. “Mr. Khamenei argues that [this government] has not done a good job and it is not prudent to reappoint them. We discussed it at length, but got no results. His real problem is the Imam’s expressed views.”

In his memoirs, Nategh-Nouri wrote about his own conversations with Rafsanjani, as well as Rafsanjani’s worries about Khamenei’s fate. “I said ‘Mr. Hashemi, it is a very bad situation. Please solve the issue of the premiership. On one hand the Imam says it must be Mr. Mousavi, and on the other, Mr. Khamenei says that if this is what Imam thinks, then he should issue a decree...This issue must be resolved.' Mr. Hashemi was very worried as well and said ‘if things continue this way, Mr. Khamenei will be badly damaged.’”

“It would be treason!”

Nategh Nouri writes that Rafsanjani agreed to meet Khomeini in the company of three figures opposed to Mousavi—Mohammad Reza Mahdavi Kani, who had acted as prime minister for close to two months in 1981, and the conservative clerics Ahmad Jannati and Mohammad Yazdi—to ask his advice. According to Nategh Nouri, Rafsanjani pleaded with Khomeini to accept Khamenei’s suggestion and issue a decree ordering him to appoint Mousavi. Khomeini refused, but remarked, “As a citizen, I pronounce that choosing anybody besides [Mousavi] is treason to Islam.”

When it became clear that Khomeini would accuse Khamenei of treason if he continued to resist Mousavi’s appointment, the intermediaries warned him about the situation. “We went to see Mr. Khamenei…We explained the situation and said this amounts to a decree. The Imam did not use the word decree…but when he says that anybody but Mousavi is treason then it is a decree.”

Rafsanjani writes that on September 16, Khomeini’s son Ahmad told him, “Today Messrs. Mahdavi Kani, Nategh Nouri, Yazdi and Jannati waited on the Imam and asked him to take back what he had said… so that Mr. Khamenei could appoint somebody else. But the Imam did not consent.”

Khomeini had taken a clear position, but Khamenei would not relent. The same day, he made a speech parliament criticizing Mousavi again. Mousavi’s supporters on the “Islamic Left” reacted strongly. “Around 80 representatives who support Mr. Mousavi’s government came and criticized yesterday’s statements by Ayatollah Khamenei,” Rafsanjani wrote the next day. “They have prepared a letter to the Imam and are gathering signatures.”

Out of 267 MPs, 135 signed the letter. Khomeini held firm in his written reply. “This written confirmation must make Mr. President and the faction opposing Mr. Mousavi angrier than ever,” Rafsanjani wrote.

In his written answer, Khomeini reaffirmed the right of the president and the parliament to choose the prime minister but added that in his view, replacing Mousavi was not in the best interests of the Islamic Republic. “I am obliged to express my views, so in answer to the gentlemen who asked for my views…I said that I consider Mr. Mousavi a devout and committed person and believe that his government has been successful in the current complex situation of the country. At present, I do not believe it wise to change the government. But the right to choose [the prime minister] rests with the president and the Islamic Consultative Assembly.”

Surrender without Grace

After Khomeini had publicly announced his position, Khamenei had no choice but to defer to him. Against his own wishes, Khamenei presented Mir Hossein Mousavi to parliament on October 10, 1985. Rafsanjani, who as speaker had been supporting Khamenei against leftist MPs, tried to calm the situation. “I praised Mr. Khamenei a lot to counter the efforts in recent weeks to weaken him,” he wrote.

But Khamenei could not suppress his hostility toward Mousavi. In his speeches, he continued to allude critically to Mousavi’s government. Khomeini found this irritating. His son Ahmad “came and said that Mr. Khamenei’s speech the day before yesterday has irked the Imam… the Imam wants to give him a message about this, Rafsanjani wrote on October 12. “

The content of the message is unknown.

“Not 99 but 100”

On October 13, parliament was set to give the prime minister its vote of confidence. “Of 267 representatives, 261 were present,” Rafsanjani wrote. “Of these, 162 voted yes, 73 voted no, and 26 abstained. Most MPs were very unhappy about the 99 votes [against Mousavi] because they went against the wishes of the Imam.”

The next day, Ahmad Khomeini told Rafsanjani that his father had advised Khamenei to stop criticizing Mousavi’s government and get rid of the “bad company” around him. “Mr. President has accepted,” he wrote.

The story of the 99 MPs who refused to give Mousavi a vote of confidence and defied Khomeini’s wishes remained a sore point for Khomeini’s followers for a long time. But ever since, Khamenei has praised those who supported his struggle against Mousavi. In a 1986 speech on the anniversary of the founding of the Islamic Republic Party, he went so far as to announce that he himself had voted against Mousavi.

The Not-So-Magnificent Obsession

Khamenei’s obsession with Mousavi was so intense that he challenged the prime minister right up until the end of Khomeini’s life. In a 1988 speech to Revolutionary Guards commanders in Ahvaz, near the battlefields of war with Iraq, he said, “Since responsibility for the government does not rest with me but with the prime minister, I am not responsible for the war and the government’s actions…I do not approve of Mir Hossein Mousavi. I accepted him because the Imam ordered it.”

Two months later, Mousavi offered to resign because he believed his government did not adequate powers. He wrote a confidential letter to Khamenei complaining that the government had been “stripped of its powers in foreign policy.” This letter was published in the official newspaper Iran during the 2009 presidential elections. Before then, only government insiders had been aware of its existence.

“Today the relations with Afghanistan, Iraq and Lebanon are under the control of your excellency,” Mousavi wrote. “Letters are written to various countries without the knowledge of the government. As prime minister, I have had no knowledge of these letters apart from exceptional cases, and then only by accident…Mr. [Mohammad Javad] Larijani [deputy foreign minister at the time] has said that there are five channels of communications with the US, but I have no knowledge of them although I am the head of the cabinet…Everywhere they talk about the foreign policies of the Islamic Republic but the government knows nothing about them.”

“Extraterritorial operations,” Mousavi wrote, “are conducted without the knowledge of the government. “You are well aware of how many disasters this has created, and of their unpleasant consequences for the country. We learn about them only when a machine gun begins firing in a street in Lebanon and the news is heard everywhere. It is only after they seize explosives from our Haj pilgrims in Jeddah that I learn about it. Unfortunately, in spite of all the damage that they have done to the country, such operations in the name of the government can happen at any moment.”

Mousavi concludes that he cannot answer for actions done in the name of the government without its knowledge, and that under such conditions, he cannot continue to take responsibility. The letter is dated October 6, 1988, one day after Mousavi officially submitted his resignation to the president.

But Khomeini himself admonished Mousavi over his resignation and advised him not to make decisions when he is angry, since “enemies of Islam” could exploit his actions. Mousavi retracted his resignation.

The Ideological Divide

The roots of the crisis remain obscure. The most important reason behind the Khamenei-Khomeini split appears to be Khamenei’s personal dislike of Mousavi, but there may be ideological reasons, too.

Khomeini was closer to the left-leaning elements of the newly-formed Islamic Republic, and Mousavi was one of their prominent figures. Khomeini took a public position in the clash between left and right factions over the powers of government.

The row started in 1987 when Mousavi’s allies and opponents disagreed over labor laws. Mousavi’s allies believed that the government had the right to require employers to obey certain regulations in their dealings with workers and employees. His opponents believed the government's intervention in labor relations was against Islamic law.

To settle the dispute, on Mousavi’s Labor Minister Abolghasem Sarhaddizadeh asked Ayatollah Khomeini to clarify the issue on December 7, that year. He wanted to know whether the government could regulate labor-management in return for providing services such as water, electricity, fuel and roads to factories and workshops. Khomeini’s answer was yes.

In reaction to Khomeini’s fatwa, the right-leaning Ayatollah Lotfollah Safi Golpayegani, who was then the secretary of the Guardian Council, wrote to Khomeini expressing concern that the government would use his fatwa to intervene in the economy outside the framework of traditional Islamic law. In January 1988, Khomeini merely reaffirmed his fatwa.

Khamenei stepped into the arena to defend right-wing faction’s views. In a Friday Prayers sermon, he announced that, although Khomeini had said that “the government can require the employer to observe a series of regulations and duties, this does not mean that accepted Islamic decrees are no longer valid…the Imam has said that the government can order the employer to observe certain conditions, but the conditions must be within the framework of accepted Islamic decrees.”

Khamenei’s statements prompted Khomeini to issue a rebuke that was carried by state-run radio and TV.

Khomeini told Khamenei that, contrary to what he had said, the powers of the Islamic state were unlimited. “It appears from your statements at Friday Prayers that your excellency does not consider the government as the absolute guardianship bestowed by God to his prophet," Khomeini said. "[Your] interpretation that the government is bound by [sharia] is completely contrary to what I said. Whatever has been said or being said is a result of not understanding the absolute divine guardianship. The government, which is a branch of the absolute guardianship of [the prophet Muhammad], is the primary decree of Islam."

Eventually, Khamenei sent a message to Khomeini saying that he accepted everything he had said.

The About-Face

Being accused by the founder of the Islamic Republic of failure to understand the nature of Islamic government was a heavy blow to Khamenei. Even so, when he became supreme leader, he fully implemented Khomeini’s theory of the Islamic state, including the primacy of such a state over all other sharia principles.

Nothing illustrates Khamenei’s understanding of his powers as the guardian of the Islamic Republic better than his ruthless crackdown on pro-Mousavi protesters following Iran's 2009 presidential elections. How could he ever forget that the same Mousavi had seen him humiliated in such a fashion?