Iran's acting charge d'affaires Hameed Shafee Zad was handed an official letter protesting the "blatant interference" in Bahrain's internal affairs, BNA reported late on Saturday.
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Khamenei's remarks "carry an explicit incitement and reflect a clear determination to foment discord and fuel tensions in the region," BNA quoted foreign ministry undersecretary Abdulla Abdullatif Abdulla as saying.
The protest by the Sunni-ruled kingdom appeared to refer to remarks posted on Khamenei's Twitter account accusing Bahrain's "tyrant minority" of "desecrating" things sacred to the Shia majority.
Bahrain has repeatedly accused Shia power Iran of meddling in its internal affairs. Last month it recalled its ambassador from Tehran and asked Iran's envoy to leave over such claims.
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Bahrain has been hit by unrest since a Shia-led uprising in 2011 that called for democratic reforms.
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