Security forces intervened in the village of Diraz, west of the capital, where protesters have been staging sit-ins since authorities revoked Sheikh Isa Qassim's citizenship in June.
He is accused of sowing sectarian divisions in the Shiite-majority Gulf archipelago, home to the US Fifth Fleet.
A 21-year-old man was hospitalised with a bullet wound to his head after the raid, human rights campaigners said quoting a medical source.
Signup to our newsletter and follow us on Facebook and Twitter!
Dozens of residents in Diraz later staged a protest chanting slogans hostile to the authorities, witnesses said.
The trial of the 75-year-old cleric on charges of illegal fundraising and money laundering opened in July. A new hearing is scheduled for Monday.
Qassim has also been accused by the interior ministry of "serving foreign interests" -- an allusion to Shiite-dominated Iran.
Bahrain has been rocked by unrest since security forces crushed Shiite-led protests demanding a constitutional monarchy and an elected prime minister in 2011.
The head of the Shiite opposition, Sheikh Ali Salman, was arrested in December 2014 and sentenced to nine years in prison after being convicted of inciting hatred.