“Unfortunately during the encounter, three members of the sect were killed while four soldiers sustained various degrees of injuries,” the army said in a statement on Monday night.
Six members the IMN sect have been killed in demonstrations since Saturday amid concerns about further crackdowns on the group.
On Saturday, three IMN members were also killed during protests in Abuja. The army claimed the protesters attacked a military convoy and tried to steal weapons and ammunition.
Monday’s clashes happened at a checkpoint as security services stopped the protesters coming into the city.
AFP photographs of the aftermath showed several bodies of civilians on the ground near police but it was not clear whether they were dead or injured.
IMN spokesman Ibrahim Musa said they had received four bodies but indicated the death toll could be higher as “scores” of people were injured and troops took away others.
“We’re trying to verify the number,” he told AFP.
Human rights group Amnesty International said reports that troops fired live bullets at protesters were “very disturbing” and would be unlawful if they were unarmed.
The IMN has staged a series of protests demanding the release of its leader Ibrahim Zakzaky, who has been in custody since December 2015 after clashes in the northern city of Zaria.
Then, the military was accused of killing more than 300 IMN supporters and burying them in mass graves.
Zakzaky has been at loggerheads with Nigeria’s secular authorities for years because of his calls for an Iranian-style Islamic revolution. Northern Nigeria is majority Sunni Muslim.
The cleric, who is in his mid-sixties and lost the sight in one eye during the 2015 clashes, has only been seen in public twice since he was detained.
Nigeria’s government has previously ignored a court order to release Zakzaky and his wife.
In April, at least 115 IMN supporters were arrested during protests in Abuja during which police used teargas and water cannon.