The trial comes amid a bitter diplomatic spat now approaching its seventh month pitting Bahrain and its allies against Qatar, which is accused of being too close to Iran.
Salman, who has been behind bars since 2014 serving a nine-year sentence on charges of inciting hatred, had refused to appear in court for a first planned hearing in the new trial on Monday.
"Sheikh Ali denied the charges levelled against him," a judicial source told AFP.
Salman and two members of his banned Al-Wefaq movement, Hassan Sultan and Ali al-Aswad -- neither of them in custody -- are charged with "communicating with a foreign state to commit acts hostile to the state of Bahrain".
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In August, Bahraini authorities accused Salman of having collaborated with Qatar in 2011 to encourage protesters to take to the streets.
The accusations came after Bahrain, along with Saudi Arabia, the United Arab Emirates and Egypt, cut ties with Qatar in June over alleged support for Islamist extremism and ties with Shiite-dominated Iran. Doha denies the allegations.
The archipelago, which is located between regional arch rivals Iran and Saudi Arabia, has been rocked by protests demanding an elected government since 2011.
Al-Wefaq was the largest party in parliament before the demonstrations erupted but its members all resigned in protest at their bloody suppression.
Over the past six years, Bahraini authorities have tightened their grip on all dissent, jailing dozens of high- profile activists and disbanding both religious and secular opposition groups.
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