Iran`s Foreign Minister Mohammad Zarif had earlier contacted his Nigerian counterpart Geoffrey Onyeama to express his "deep concern" about Saturday`s events in the city of Zaria.
ISNA said at least 12 people were killed, with both sides blaming each other.
The Nigerian military said one of its convoys was attacked by followers of Ibrahim Zakzaky, the leader of the IMN.
"The sect numbering hundreds carrying dangerous weapons, barricaded the roads with bonfires, heavy stones and tyres," an army statement said.
"The troops responsible for the safety and security of the Chief of Army Staff, on hearing explosions and firing, were left with no choice than to defend him and the convoy at all cost."
The Iranian news agency said initial clashes were followed by an army raid on Zakzaky`s home, which left several of his followers dead.
Nigeria`s Muslim population is largely Sunni but the number of Shia Muslims has increased significantly in the past three decades
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