Sheikh Isa Qassim is accused of collecting funds illegally and has deposited more than $10 million in his private bank accounts, attorney general Haroun al-Zayani said in a statement on the official BNA news agency.
Qassim, considered the spiritual leader of the majority Shia community in Bahrain, allegedly kept other amounts in cash to avoid legal controls, said the statement, accusing him of hiding the source of the money.
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Authorities also accused him of purchasing properties worth more than one million dinar ($2.65 million) in an attempt to legitimise the funds.
Two of his aides, Sheikh Hussein Mahrus and Mirza al-Obaidli, are also on trial in the same case.
The three defendants did not appear in court for the hearing, held amid tight security, witnesses said.
The next hearing will be on August 14.
On June 20, Bahrain said it had revoked Qassim's citizenship, accusing him of sowing sectarian divisions.
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Since then dozens of Shias have staged a sit-in outside his home in the village of Diraz, which authorities have cordoned off.
The move against Qassim prompted criticism from Bahrain's Western allies as well as its foe Iran, which the kingdom accuses of fuelling unrest among its Shia community.
Bahrain has been shaken by unrest since security forces crushed Shia-led protests demanding a constitutional monarchy and an elected prime minister in 2011.
Despite repeated calls from their Western allies, Bahrain's rulers have made no concessions to the Shia opposition and have intensified a crackdown on critics.
This month, a court ordered the dissolution of the kingdom's main Shia opposition bloc, Al-Wefaq, which was the largest group in parliament before its lawmakers resigned en masse in protest at the crushing of demonstrations.
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