Nigerian troops on Monday evacuated the bodies of Shiite Muslims killed in two days of clashes with the army in Northern Zaria, its spokesman and residents told AFP.
The army carried out crackdowns on Saturday and early Sunday against the IMN and have 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 said.
Musa also said Zakzaky had been arrested.
"Sheikh Ibrahim Zakzaky was arrested this morning in his demolished home by soldiers where he had been holed up in a room that was spared from the fire that gutted the house from grenades," he said.
Northern Nigeria is majority Muslim and largely Sunni.
Musa said the victims of the fighting included his wife, son and the former IMN spokesman.
"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.
He said the group's leader had been unable to leave the house "because of the gunshot wounds he sustained in the indiscriminate fire soldiers opened on the house and his followers who tried to protect it," he said.
"We gathered he was taken to Kaduna (70 kilometers, 45 miles away). We got in touch with the medical doctor that is treating him who confirmed to us that our leader is critically ill from four gunshot wounds he sustained," he said.
"He was shot at four times, this the doctor confirmed," Musa 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 said.
"A large number of his followers were gunned down around his house on Saturday through Sunday 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 latest violence was sparked when Shiite faithful on Saturday blocked the main road outside their Husseiniyya religious center, where hundreds had gathered for a ceremony.
The military claimed Shiites attacked the convoy of the army chief, Yusuf Buratai, which left soldiers no option but to retaliate.
The group however denied the claim.
Nigeria is fighting a six-year-old Boko Haram insurgency that has killed some 17,000 people and forced 2.6 million to flee their homes. IMN is among the groups standing against Boko Haram terrorists.