The ministry slammed Amnesty International over allegations of extrajudicial killings by the government.
Sheikh Ibrahim Zakzaky was arrested after deadly clashes killed almost 350 of his followers.
The country's Shiite minority has had several high-profile conflicts with Nigerian security forces.
Kaduna's state government declared the Islamic Movement in Nigeria to be unlawful on Friday.
More than 300 people were reportedly killed in December's clashes between Shiites and the army.
A government official admitted that 347 Shiites were buried in a mass grave after Nigerian army clashes.
Sheikh Zakzaky's lawyer is demanding his client's unconditional release after four months in detention.
The Islamic Movement in Nigeria say they have no ties to the Sunni militant group.
The Nigerian Shiite leader was arrested in December 2015 and is being held without charge.
Nigerian Shiites clashed with the army in December, with 300 sect members reportedly killed.
The Shiite leader has been detained since December, when soldiers clashed with Shiite sect members.
At least 300 Shiites were killed in clashes with the army in Zaria, northern Nigeria.
At least 60 people died in clashes between Shiite Muslims and Nigerian soldiers on Saturday.
The Shiite movement claims dozens of its members were killed by soldiers on Saturday.
At least 21 people were killed when a suicide bomber detonated explosives during a religious procession near Kano.