Amnesty called for the immediate and unconditional release of Sheikh Ali Salman, the head of the influential Al-Wefaq bloc who was arrested on December 28 on charges including seeking regime change.
In a statement, the group said it considers Salman's detention "a flagrant violation of his right to freedom of expression, association and assembly" and urged the Bahraini authorities "to release him immediately and unconditionally".
"If convicted, the organisation would consider him a prisoner of conscience," the London-based watchdog said.
Salman was remanded in custody on Monday for two more weeks pending investigation.
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Prosecutors allege that Salman confessed to contacting foreign regimes and political groups abroad, some of whom had "expressed readiness" to interfere in Bahrain's affairs.
Iran has been accused of interfering in Bahrain since its Sunni ruling family crushed month-long protests led by Al-Wefaq in 2011 seeking an elected government in the Shiite-majority kingdom.
Shiite-dominated Iran has criticised Salman's detention.
The United States also expressed deep concern, warning the detention could inflame the persistent violence that has gripped the kingdom, which is home to its Fifth Fleet.
At least 89 people have been killed in clashes with security forces since the protests were crushed.
Hundreds have also been arrested and put on trial, human rights groups say.