The testimony today from Muhammad Namadi Musa, the director-general of the Kaduna State religious affairs office, lends weight to claims that at least 300 people were killed in the violence in December last year.
Amnesty International, which has previously said "hundreds" were killed, said the revelation was "an important first step in bringing all those suspected of criminal responsibility" to trial.
"It is now imperative that the mass grave sites are protected in order that a full independent forensic investigation can begin," said the organisation's Nigeria director, M.K. Ibrahim.
The clashes came after the army said supporters of the cleric Ibrahim Zakzaky, who heads the pro-Iranian religious sect Islamic Movement of Nigeria (IMN) group, tried to kill the chief of army staff.
Zakzaky has not been seen since his home and the IMN mosque in Zaria, Kaduna state, were destroyed, prompting calls for his release and criticism that the government is flouting due process.
Musa said told the hearing he was ordered on December 13 to travel to Zaria with the Kaduna state commissioner of police "to find out the number of corpses and how they would be buried".
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