Mohammad Jafar Montazeri ordered the shutting down of Sedayeh Eslahat for “desecrating” the family of Prophet Muhammad’s grandson, Imam Hussein, the Fars news agency reported on Friday.
The article that caused offence was about a female-to-male gender reassignment surgery, according to The Associated Press, which cited Iranian media reports.
It was published on the newspaper’s front page on Thursday and carried the headline: “Ruqayyah became Mahdi after 22 years”.
Ruqayyah was the daughter of Hussein and the article was published during Muharram, a holiday in which Shia Muslims mourn the Imam’s death.
According to Shia Islam, Mahdi is the name of the 12th Shia Imam who has lived since the 9th century.
In a letter published by Fars, Montazeri said the article caused “protest during these days of sorrow”, and ordered the editor of Sedayeh Eslahat be punished over its publication.
Iran is ranked 164th out of 180 countries in Reporters Without Borders’ (RSF) press freedom index.
In August, Iranian courts jailed seven journalists and ordered them to be flogged publicly over their coverage of protests by the Dervish minority.
The Committee to Protect Journalists said the “horrifying sentences laid bare Iranian authorities’ depraved attitude toward journalists”.