"Amnesty International is calling on the Nigerian authorities to investigate all cases of enforced disappearances and bring all those suspected of criminal responsibility to justice," the group said in a statement.
"According to figures provided by the IMN, at least 600 of their members' whereabouts is not known."
More than 350 IMN followers, led by prominent Sheikh Ibrahim Zakzaky, were martyred in a heavy military crackdown in the northern town of Zaria in December 2015.
Sheikh Zakzaky, who was shot and injured leaving him partly paralyzed and blind in one eye, remains in protective custody, according to the military.
He has repeatedly been imprisoned for alleged incitement and subversion.