Bahrain’s foreign ministry has summoned Iran’s charge d’affaires in Manama to protest at what it described a “gross violation of its sovereignty”.
It follows official Iranian calls for demonstrations against a proposed union between Saudi Arabia and Bahrain.
A summit of the Gulf states discussed the proposal on Monday but did not reach any decision on the matter.
Bahrain’s Sunni royal family has accused Iran of supporting mass protests by the nation’s Shia majority.
The proposed union was presented as a first step in a larger integration between all six Gulf Co-operation Council (GCC) members.