Muntadher Ali Saleh al-Sabity was detained on Thursday evening in an operation in the town of Awamiya, the official SPA news agency quoted a ministry spokesman as saying.
Sabity is one of 23 Saudis wanted in connection with protests and violence in Eastern Province, home to more than two million Shiites in the Sunni-majority kingdom.
The group, some of whom have been detained or killed, is accused of acting "on behalf of foreign parties" -- a reference to Iran, which authorities have blamed in the past for fomenting unrest among Saudi Shiites.
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Most live in the oil-rich east, and many complain of marginalisation.
Protests erupted in Eastern Province in February 2011 after an outbreak of violence between Shiite pilgrims and religious police in the Muslim holy city of Medina in western Saudi Arabia.
Awamiya, just west of Dammam city on the Gulf coast, has witnessed clashes between security forces and protesters.
Earlier this month, a court sentenced to death a man who opened fire numerous times on police in the town.