Ministry spokesman Hossein Jaber Ansari strongly condemned the execution, which came after his Shiite country repeatedly asked its Sunni-ruled rival to pardon the cleric.
"The Saudi government supports terrorist movements and extremists, but confronts domestic critics with oppression and execution... The Saudi government will pay a high price for following these policies," he said, quoted by the official IRNA news agency.
Nimr, 56, was a driving force of the protests that broke out in 2011 in Eastern Province, where the Shiite minority of Saudi Arabia complains of marginalisation.
For its part, the Basij student militia connected to Iran's elite Revolutionary Guards called for a demonstration on Sunday afternoon in front of the Saudi embassy in Tehran.
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