The authorities also plan to close down the internet site on which Sheikh Mohamed Ben Abderrahman Al-Maghraoui decreed earlier this month that the marriage of nine-year-old girls is allowed by Islam.
The sheikh said his decree was based on the fact that the Prophet Mohammad consummated his marriage to his favourite wife when she was that age.
Lawyers, the media, and finally Muslim scholars rounded on Maghraoui for effectively seeking to legalise paedophilia.
The authorities finally took action on Wednesday, shutting down his headquarters in Marrakesh and dozens of his small Qur'anic schools dotted around the country.
"The internet site 'Maghrawi.net' is going to be closed, while the headquarters of the Mohamed Maghraoui association in Marrakesh and his 'Qur'anic Houses' have already been closed," a security official said.
Sheikh Maghraoui's 'fatwa' or religious decree was condemned on Sunday by Morocco's top body of Islamic scholars.
The High Council of Ulemas, which is presided over by Morocco's King Mohammed VI, labelled the sheikh an "agitator" and denounced his "utilisation of religion to legitimise the marriage of nine-year-old girls".
Rabat-based lawyer Mourad Bekkouri filed a complaint against Maghraoui and his fatwa earlier this month in which he said the decree damaged children's rights by increasing the risk of rape.
He said the theologian is undermining Islam and its followers and that he had requested the state prosecutor to speed up the case.