The most prominent Shia religious leader of the time, Grand Ayatollah Abu al-Qasim al-Khoei, sought to dismiss Al-Shirazi's status as a scholar.

According to Cambridge University's Toby Matthiesen: "The political theory of Muhammad al-Shirazi and the MVM [Movement of Vanguard Missions] was quite close to Khomeini’s notion of velayet-e faqih (the guardianship of the jurisprudent), although al-Shirazi favored the theory that not a single cleric, but a council of scholars should govern the Islamic State (hukumat al-fuqaha’/shurat al-fuqaha’).

"[6] Under al-Shirazi's theory government would be in the form of a 'Consultative System of Leadership' composed of senior clerics, and he called for the establishment of the 'Leadership Council of Religious Authorities'.

As the radicals were increasingly sidelined by the more moderate Sayyid ‘Ali Khamenei and ‘Ali-Akbar Hashemi Rafsanjani, Al-Shirazi's influence waned.

In January Sheikh Mohammad Amin Ghafoori, a well-known religious figure and writer, his wife, and Sayed Hossein Fali were arrested in Qom.

Sheikh Mohammad Amin Ghafoori was said to have been sentenced in July to two and a half years' imprisonment by the Special Court for the Clergy, whose procedures fell far short of international standards.

In October, five other followers of Grand Ayatollah Shirazi, including Reza Sultani, were reported to have been arrested and they remained held incommunicado at the end of the year.

Sheikh Sadiq Za'eemiyan has also been harassed.Seven students arrested in November 1995, apparently on account of their links with Grand Ayatollah Shirazi (see Amnesty International Reports 1996 and 1997), were released in June.

[10]According to reports, methods of torture used against some of these detainees have included beatings, prolonged sleep deprivation, electric shocks and threatened execution by electrocution after attaching electrodes to the body.

Sheikh Ali Maash is said to have required medical treatment after his release for the effects of torture, including for a toe on his right foot which was broken and left untreated.

[13] Al-Shirazi has written on different subjects including science, ethics, politics, economics, sociology, law, human rights, etc.

A bid by Assad Ali to get the Guinness World Records to recognise Muhammad al-Shirazi as the most prolific writer in Arabic was rejected by the publisher.

[15][16] Although he was under house arrest for a long time, people who often saw him said he never insulted the former supreme guide, Khomeini, or the current one, Ali Khamenei, although his relations with them were not good.