Sheikh Isa Qassim, who is considered the spiritual leader of Bahrain's Shiite majority, was alleged to have used his position to "serve foreign interests and promote... sectarianism and violence," the ministry said in a statement carried by BNA state news agency.
It comes days after a regime’s court issued an order earlier suspending the activities of Bahrain’s main opposition bloc, Al-Wefaq National Islamic Society, on charges of “terrorism, extremism, and violence”.
Bahrain, a close ally of the US in the Persian Gulf region, has been witnessing almost daily protests against the ruling Al Khalifa dynasty since early 2011, with Manama using heavy-handed measures in an attempt to crush the demonstrations.
Scores of Bahrainis have been killed and hundreds of others injured and arrested in the ongoing crackdown on the peaceful demonstrations.
Amnesty International and many other international rights organizations have frequently censured the Bahraini regime for the rampant human rights abuses against opposition groups and anti-regime protesters.