Witnesses say soldiers fired at the students as they marched toward the troops Friday, upset over the deaths of fellow classmates in recent Christian-Muslim violence.
A student leader told the Associated Press that two students died in the violence — one stabbed by a rioter and another shot dead. Military officials say they had no information about any deaths in the shootout.
Police say sectarian clashes near Jos on Thursday killed 12 people.
Jos is located in Nigeria's so-called middle belt, where the mostly Muslim north meets the mainly Christian south and has been plagued by sectarian violence.
Nigeria's 140 million people are divided roughly evenly between Christians and Muslims. Periodic clashes between the groups, mostly in and around Jos, have killed thousands of people in recent years.