Sheikh Ali Salman, head of the Shiite movement Al-Wefaq, was charged on Monday by authorities in the tiny Sunni-ruled nation, where the opposition boycotted a November parliamentary election that it dismissed as a farce.
The prosecution said Tuesday the cleric would remain in custody for seven days pending further investigation.
Bahrain has been gripped by sporadic violence since the authorities crushed month-long pro-democracy protests led by Al-Wefaq in 2011.
At least 89 people have been killed since then in clashes with security forces, and hundreds arrested and put on trial, human rights groups say.
Al-Wefaq denounced Salman's detention, saying it "entrenches the tyrannical rule in Bahrain and closes all doors for a political solution."
"This behaviour is dangerous and reflects the magnitude of the political crisis between the regime and the people, and shows that Bahrain needs a political plan under which power would be in the hands of the people," it said.
Salman's arrest Sunday triggered clashes between police and protesters in Shiite villages outside the capital Manama, during which security forces fired tear gas to disperse demonstrators, and which carried on into the next day.
'DON'T MIX RELIGION, POLITICS'
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Police again fired tear gas Tuesday during clashes with young protesters gathered outside the cleric's house in a Shiite suburb of the capital, and witnesses said five people were wounded.
Violence was also reported in other villages.
It came after Salman was re-elected as party leader on Friday.
The prosecution said Monday that Salman, 49, had been charged with "promoting regime change by force, threats and illegal means and of insulting the interior ministry publicly."
Prosecutor Nayef Mahmud said in a statement that Salman was also accused of inciting people to break the law and of "hatred towards a segment of the people", an allusion to Sunni Muslims who are a minority in the Shiite-majority kingdom.
The prosecutor said police also suspect Salman of calling for foreign interference by "urging super powers to intervene in Bahrain to support him in his bid to change the regime."
The prosecution continued questioning Salman Tuesday and presented him with "recordings of his incitements, which justified violence and threats," Mahmud said.
Meanwhile, the justice and Islamic affairs ministry warned Al-Wefaq against using mosques and religion for political purposes.
Al-Wefaq's "implication of clerics in politics is a dangerous deviation from the principles of political work," a statement said, while urging the group to "respect the law."
Strategically located just across the Gulf from Iran, Bahrain is home to the US Navy's Fifth Fleet, and Britain announced plans earlier this month to build a naval base of its own there.
The authorities have rejected Al-Wefaq's demand for an elected prime minister to replace the current government dominated by the ruling royal family.
After Al-Wefaq announced that it would boycott the November election, a court banned the movement from activities for three months for violating the law on associations.