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The Hierarchy of the Iran 1988 Massacre


The chief henchman and principal perpetrator of the 1988 massacre was the regime’s former supreme leader Khomeini himself.
On August 6, 1988, Khomeini responded to a letter sent from his heir apparent at the time, Ayatollah Hossein-Ali Montazeri. Khomeini responded to the letter using his son Ahmad as an intermediary. In the letter, Khomeini stressed: “Under Sharia law, the responsibility for issuing the decree in question is mine. So, you do not have to worry. May God rid us all of the evil of the Monafeqin [PMOI/MEK].” (As published in Hossein-Ali Montazeri’s Memoirs (in Farsi), Chapter 10. Date of publication: 2000.)

In addition to the initial decree, which triggered the massacre, Khomeini issued a series of other directives in the subsequent phases of the massacre, encompassing several dimensions, including political, administrative, and Sharia.
Khomeini’s commands for executions were implemented through an organizational hierarchy responsible for executions on the ground. At the highest level below Khomeini, those who ensured the implementation of Khomeini’s commands and directives were his son, Ahmad, then-president and current supreme leader Ali Khamenei, and then-speaker of parliament Ali Akbar Hashemi Rafsanjani.

hmad Khomeini (left), Ali Khamene (center)i, Ali Akbar Hashemi Rafsanjani (right)
Ahmad Khomeini (left), Ali Khamenei (center)i, Ali Akbar Hashemi Rafsanjani (right)

In December 1988, when then-president Ali Khamenei was questioned by Tehran university students in this regard, he positioned himself as a decision-maker and defended the executions.

According to state-run press reports at the time: “At a warm and cordial meeting with university students, Hojjat ol-Eslam Khamenei responded to some of the most important and fundamental questions floating in university circles. … He was asked ‘what is behind the Islamic Republic’s disregard to the issue of human rights and preventing human rights experts of the UN to investigate this matter? What are the reasons for the extensive executions in Iran, in Tehran and the provinces?’ In response, the president said: ‘The tone of your question resembles the tone heard in the recent statements made by foreign radio stations. Still, this is a question and I’ll respond to it. We do not disregard the human rights issue. … Those who make statements against us around the world concerning human rights want the Monafeqin [PMOI/MEK] and all those who seek the overthrow of the establishment in this country to do whatever they please without the establishment reacting in the slightest way. This is in contradiction to the interests of the people and the establishment. The Monafeqin [PMOI/MEK] has created some of the worst tragedies in the country since the beginning of the revolution. Amnesty International and the UN Human Rights Commission did not utter a word. … My brother! this is a political thing! And concerning the executions: This is exactly the same interpretation heard from foreign radio stations. The Monafeqin’s [PMOI/MEK] radio says the same thing. Have we banned the death penalty?! Like many other countries in the world, we carry out the death penalty. For whom? For those whose crimes deserve the death penalty. We will execute anyone who commits these types of crimes, regardless of family ties or foreign links. In your opinion, should we hand out sweets and candy to a person who while in prison has links to the Monafeqin [MEK]? The MEK has conducted an armed incursion into the Islamic Republic territory while triggering tragedies alongside a foreign enemy in Eslam Abad, Kerand, and similar places. What should be done if the person’s links to that treacherous system are made clear? In our view, they are sentenced to death and we will execute them.” (State-run Resalat daily, December 7, 1988.)


Supreme Judicial Council


Abdul-Karim Moussavi Ardabili (deceased 2016), at the time president of the Supreme Judicial Council, and the members of this council, officially formed the next level of command in the hierarchy although they did not act as fast as Khomeini would have preferred. At the time, members of the Supreme Judicial Council and their position titles were:


Morteza Moqtadaee, spokesperson and of the Supreme Judicial Council and member of the Assembly of Experts since the time of the 1988 executions to the present.


Seyyed Mohammad Moussavi Bojnourdi, member of the Supreme Judicial Council.


Seyyed Mohammad Hassan Marashi Shushtari (deceased 2008), member of the Supreme Judicial Council.


Mohammad Moussavi Khoeiniha, Member of the Supreme Judicial Council and Prosecutor General heading the country’s prosecutors’ offices
Concerning Khoeiniha’s role in the massacre, the French daily Le Monde wrote several months after the launch of the massacre: “Imam Khomeini, summoned the Revolution’s Prosector, Hojjat ol-Eslam Khoeiniha, to issue an order that from this point forward, all PMOI/MEK/, in prisons or other places, must be viewed as Mohareb [enemies of God] and must be killed as a result.” (French daily Le Monde, March 2, 1989)
In the so-called judicial hierarchy, under the Supreme Judicial Council, were the death commissions in provincial capitals and some cities. Their role was to identify prisoners who are still “committed” to their political views and to then send them to death corridors. In practice, however, these commissions were directed by the Intelligence Ministry, which was itself an instrument at the hands of Khomeini himself.
Among these commissions, the special Tehran death commission, which included Hossein-Ali Nayyeri, Morteza Eshraqi, Ebrahim Raeesi, and Mostafa Pour-Mohammadi, enjoyed significantly more influence compared to other commissions. In many cases, the Tehran death commission practically circumvented the Supreme Judicial Council and obtained its orders directly from Khomeini.

Ministry of Intelligence and Security (MOIS)

The main director of the massacre was the Iranian regime’s Ministry of Intelligence and Security (MOIS). At its helm was Mohammad Mohammadi-Nik (aka Reyshahri).


He got his orders directly from Khomeini and in turn reported back to Khomeini personally.
Since then, Reyshahri has continued to occupy important posts in the regime. He once ran for president and is currently a member of the Assembly of Experts and the head of Shah Abdol Azim religious endowment. The endowment controls the tomb of Shah Abdol Azim located south of Tehran, who was a descendant of the third Shiite Imam Hussain bin Ali.
Reyshahri’s deputies also had a formative role in the massacre:
Reyshahri’s second-in-command, Mullah Ali Fallahian, actively managed the administrative activities related to the massacre.


In 2017, he said: “This [massacre] was based on a fatwa by the Imam [Khomeini]. … The sentence for these people [PMOI/MEK] will always be execution. This was in essence a leadership and guidance ruling, both before the 1988 development and after it. … The Imam repeatedly stressed that be vigilant so they don’t escape from you. … Imam’s view was why should we keep them alive?” Fallahian’s account of confronting the MEK in the 1980s: Even if a person buys bread for [them], they must be executed,” State-run Iran daily, July 18, 2017.
Following the 1988 massacre, Fallahian became the intelligence minister, where he led a number of criminal and notorious projects, including the assassination of Dr. Kazem Rajavi, representative of the National Council of Resistance of Iran (NCRI) in Geneva, on April 24, 1990. In 2006, a Swiss investigative judge issued an international arrest warrant against Fallahian for his role as a decision-maker in the assassination. On November 7, 2007, Argentina’s judiciary issued a warrant for Fallahian for his involvement in the 1994 bombing of a Jewish cultural center in Buenos Aires. He is also wanted by Interpol for his role in the assassination of dissident Iranian Kurds in Berlin’s Mykonos Restaurants, for which German courts have convicted him in absentia.
Another Reyshahri deputy involved in the massacre is Javad Ali Akbarian.


At the time, Akbarian managed the offices of planning, administration and financials, and foreign intelligence in the MOIS. Following the massacre, he was for a long time the deputy of the Islamic Culture and Communications Organizations, which is one of the most important institutions of the regime for exporting fundamentalism. He is currently the Reyshahri’s deputy at the Shah Abdul Azim religious endowment.

Another official, Gholam-Hossein Mohseni Ejei, was at the time the Judiciary’s representative at the MOI and also played a key role in directing the executions.


In the 1990s, Ejei also played a significant role in the so-called “chain killings” of Iranian intellectuals and writers. He was subsequently appointed as the intelligence minister (2005-2009) and the prosecutor general (2009-2014). He is currently the first deputy of the Judiciary and a member of the Expediency Council.
In 2011, the European Union placed Ejei on the list of sanctions for his role in serious human rights violations and harassment of the Iranian people during the 2009 uprisings.
The representative of the MOIS had a definitive role in all death commissions and pushed the commissions to increase the number of executions. In effect, they were the eyes, ears, and arms of the henchman. As Montazeri has said: “He [Khomeini] would receive various reports from Intelligence Ministry officials … he would treat these reports as divine truth.”
The memoirs of then-intelligence minister, Mohammadi Reyshahri, includes several letters exchanged between him and Khomeini, verifying that Khomeini directly led the ministry to carry out the crimes. In his book, Reyshahri also confesses to the suppression of Montazeri’s inner circle, saying: “We referred to him even for the smallest matters.”

The Government and Other Organs

Then-prime minister Mir-Hossein Moussavi and his cabinet ministers were the highest executive branch officials.


Therefore, they could not have had any responsibility when it came to the extensive massacre that occurred in 1988. For their part, they played a role in facilitating the machinery of the massacre, providing it with the necessary political justification and diplomatic cover. Some of the irrefutable pieces of evidence in this regard are the statements made by these officials in defense of the massacre.

In an interview with Austria’s national TV station on December 13, 1988, Khomeini’s prime minister at the time, Mir-Hossein Moussavi, was asked “What is your reaction to western media claims regarding human rights violations in Iran?” In response, Mossavi said: “Human rights must really be defined. … One of the things we are blamed for is about this Mersad operation. During this operation, a number of the Monafeqin [PMOI/MEK] carried out tremendous murder and pillage in our country in accordance with their deceitful political designs. They allied themselves with our people’s enemy, Saddam, and attacked their own country naively thinking that they can occupy Bakhtaran [Kermanshah] and later advance toward Tehran. They had designs for murder, and we were forced to suppress their plot. If we had not done this and had opened the gates of our cities toward them, we would have naturally given them a free hand in the killing and murder of our people. When it comes to these things, we show no forgiveness. Our establishment does not give itself the right to avoid defending itself or to avoid showing a firm response.” (The text of this interview was published in the state-run daily Ettelaat on December 22, 1988.)

On December 12, 2018, Amnesty International also released a report about this issue and mentioned the same interview.
Moussavi’s response was based on the pivotal tactics of the regime’s officials at that time. Most of them did not mention political prisoners and instead spoke of defending the regime against the “Mersad” operation. The political logic of this amounts to defending the massacre. In his response above, Moussavi uses phrases like “showing no forgiveness” and a “firm response,” indicating alignment with Khomeini’s fatwa ordering the MEK’s massacre. As Professor Jeffrey Robertson has explained in his opinion, by pointing to the Mersad operation in his interview with the Austrian TV, Moussavi justified or at least downplayed the significance of the killings, and therefore joined other officials and leaders of the regime.
It can also not be ignored that when on September 5, 1988, Moussavi suddenly resigned due to the crises and pressures faced by the regime, he did not exhibit the slightest displeasure or did not at least make any references to the most significant political campaign of the regime at the time, which was the eradication of all political prisoners. In his five-point resignation letter, however, he did reference problems such as the resignation of ministers, the conflict between the Majlis and cabinet nominations, the conflict with the president, and the reduction of the prime minister’s scope of authorities, among other things.
It should be noted that in 1988, the most recognizable faces of the government did not in the least remove themselves from the task of defending the massacre.


Then-interior minister, Ali Akbar Mohtashamipour, who in 2009 was also the chairman of the “Committee Safeguarding the Mir-Hossein Moussavi’s Votes.” In 1989, Reuters reported that “On Monday, Ali Akbar Mohtashamipour, Iran’s minister of interior, was quoted as saying that ‘all opponents held in Iran’s prisons have been executed.’ Mohtashami told Paris-based Arabic publication Al-Mostaqbal: ‘In order to clarify this once and for all, all those who were arrested and all those who had joined them have been executed.'” (Reuters, February 27, 1989.)


Then-foreign minister, Ali Akbar Velayati also told French daily L’Humanité in response to a question about the identities of those executed in Iranian prisons: “All those executed include people that confessed to the prosecutor that they condone with PMOI/MEK and wanted to join them to overthrow the regime. The PMOI planned to break down prison doors to free them.” (French daily L’Humanite, February 7, 1989.)

Another non-judiciary official at the time was Mohammad Khatami, who became the regime’s president in 1997. In March 2000, he ordered the closure of the Arya daily because it had made a small reference to the massacre of 1988. The editor-in-chief of the daily was sentenced to four months in prison and a heavy financial fine.
A report published by the state-run daily Resalat sheds some light on this development as well as then-president Khatami’s ties with the 1988 massacre: “Why did Arya daily get banned on the orders of the president and why did it restart its activities without any investigations into its violations? The daily Arya, which was banned by the president, has restarted its activities. … Arya’s suspension in early 2000 occurred after the publication of an interview with the Iran-e Farda editor-in-chief. In that interview, the editor-in-chief had said: ‘In my opinion, the main solution for the suspicious killings is to return to the past and reopen the case for the extensive execution of political prisoners in the summer of 1988. Everyone who participated, in that case, must as a first step be removed from their post. Lack of a government job should not only be the case for Ayatollah Montazeri. This statement points to a directive by the Imam [Khomeini] following the Mersad Operation and the full cooperation of the [PMOI/MEK] with the Iraqi regime. The imam had ordered officials to sentence to death the Mohareb [enemies of God] and Monafeq [hypocrites] who continue to insist on their enmity against the establishment and their solidarity with the MEK in accordance with Sharia law. This order was issued and implemented at a time when Mr. Khatami was the cultural deputy of the commander-in-chief of the armed forces. He had completely supported the order of the Imam. … The entire reason for the silent suspension of this Dovom-Khordadi [pro-Khatami] Arya daily was this and such was the reason also for the silence of all the other [pro-Khatami] publications, which used to create a fuss for any mistreatment of the press. Following up on this issue and shedding some light on it can be interpreted as a very negative point in the reformists’ record and for the appeasement and compromise project.” (State-run daily Resalat, April 9, 2000. The report was also published by another state-run daily named Sobh-e Iran (Morning in Iran) on April 5, 2000.)

Last but not least, it is necessary to recall Mehdi Karoubi’s statement justifying the 1988 massacre. At the time, he was the first deputy speaker of the Majlis (parliament) and the leader of the Combatant Clergy Association, which had the closest ties between the clergy and Khomeini.
On February 18, 1989, Karoubi, in collaboration with two other pro-Khomeini mullahs, Hamid Rouhani and Mehdi Jamarani, wrote a letter to Montazeri stating: “When you found out that a bunch of [PMOI/MEK] and [enemies against God] were sentenced and executed in accordance with judicial regulations, you wrote letters and also met with judicial officials where you called them criminals and this action a crime. How surprising! … Would the judicial officials of the Islamic Republic establishment be considered criminals if they sentence and execute several plotters who planned to overthrow [the regime]?” (Hossein-Ali Montazeri, Memoirs, Chapter 10, Appendix no. 167. Date of publication: 2000.)

In a 1999 letter to Montazeri’s son, Karoubi complained why he has called the massacre of PMOI members unjust. Karoubi wrote:
“Dear Ahmad, you used a shocking statement in your interview about the imprisoned Monfeqs [PMOI/MEK supporters] who had insisted on their position and were confronted accordingly. … We see that a number of them insist on their unjust positions and created a rebellion in prisons before the victory of the Islamic army during the Mersad Operation, and they beat up the prisoners who had expressed loyalty to the Islamic establishment. When these sorts of people are dealt with you refer to it as ‘blood that was unjustly shed’?” (State-run daily Jomhouri-e Eslami, August 4, 1999.)

The Expediency Council

This senior consultative body was chaired by Khamenei (as the president) at the time of the massacre. In his memoirs, former president Ali Akbar Hashemi Rafsanjani (who would later chair the body) wrote: “I went to the Expediency Council meeting. The punishment of the anti-revolutionaries was discussed. The Imam has delegated a decision to the Expediency Council. As usual, it was agreed that action would be taken before the recent incidents. This was the Intelligence Ministry’s opinion and the Evin judges had a more firm opinion.” (Ali Akbar Hashemi Rafsanjani, Track Record, and Memoirs of 1988: The end of Defense Period and the Beginning of Rebuilding Efforts (seventh edition), p. 328, 2011.)
The aforementioned meeting took place on September 28, 1988. Therefore, from that day forward, the members of the Expediency Council were responsible for decisions around the massacre. They bear the responsibility for a significant portion of this great crime. At the time, these members included: Ali Khamenei, Ali Akbar Hashemi Rafsanjani, Abdol-Karim Moussavi Ardebili, Mohammad-Reza Tavassoli, Mohammad Moussavi-Khoiniha, Mir Hossein Moussavi, Ahmad Khomeini, and members of the Guardian Council, whom at the time were: Mohammad Mohammadi Gilani, Ahmad Jannati, Abol Qassem Khazali, Mohammad Momen Qomi, Mohammad Emami Kashani, and Mohammad Yazdi.