The army carried out crackdowns on Saturday and early Sunday against the pro-Iranian Islamic Movement of Nigeria (IMN) led by Ibrahim Zakzaky, whose whereabouts were unknown, they said.
"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.
The IMN, which seeks to establish an Islamic state through an Iranian-styled revolution, has been at loggerheads with Nigeria's secular authorities, leading to occasionally violent confrontations.
"We can't give a precise figure of the deaths but it is huge given the number of the members that answered the call to protect the house from the invading soldiers," he said.
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"I can confirm that the wife of our leader Zeenat Ibrahim and her son Ali were among the dead. Our national spokesman Ibrahim Usman was also killed," he said.
The group's leader has periodically been incarcerated for alleged incitement and subversion.
Northern Nigeria is majority Muslim and largely Sunni.
"We have been getting conflicting reports with some saying that he has been taken away by soldiers while others are saying that he has been killed," he said.
Witnesses also spoke of soldiers removing bodies around Zakzaky's house.
"This morning, soldiers started evacuating corpses of followers of Zakzaky in trucks for possible disposal," resident Bashir Bello told AFP.
"A large number of his followers were gunned down around his house on Saturday through yesterday morning where they had congregated to protect the house from military invasion," he said.
He said soldiers had mounted security checks as residents and motorists were being searched before entering the area.
The military claimed the Shiites attacked the convoy of the army chief, Yusuf Buratai, which left soldiers no option but to retaliate.
The group however denied the claim.