The diplomat was told the foreign ministry yesterday that Iran "demands the Nigerian government immediately shed light on the incidents, treat the injured, and compensate for damages," IRNA said.
It said Foreign Minister Mohammad Javad Zarif also called for "immediate and serious action to prevent violence" against Shiites in a telephone call to his Nigerian counterpart Geoffrey Onyeama.
The army clashed on Saturday and early Sunday in the largely Sunni Muslim north with the Islamic Movement of Nigeria (IMN) and arrested its leader Ibrahim Zakzaky.
"We have reports that bodies of our members killed outside the house of our leader are being evacuated in trucks by soldiers," IMN spokesman Ibrahim Musa told AFP.
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Musa said victims of the violence included Zakzaky's wife, son and a former IMN spokesman.
The violence was sparked when Shiite faithful on Saturday blocked the main road outside their prayer centre, where hundreds had gathered for a ceremony.
The military claimed Shiites attacked a convoy of the army chief, Yusuf Buratai, leaving soldiers no option but to retaliate. The IMN, however, denied the charge.