The rights group claimed that nine senior commanders had overseen torture and abuses that led to some 8,000 deaths.
The group have continued to attack pipelines in the region, cutting oil production by 600,000 barrels per day.
More than 300 people were reportedly killed in December's clashes between Shiites and the army.
Nigeria has launched Operation Safe Corridor for repentant members of the ISIS-affiliated group.
The Islamic Movement in Nigeria say they have no ties to the Sunni militant group.
Colonel Samaila Inusa was found dead on Tuesday after being abducted in Kaduna two days earlier.
At least 300 people died in clashes between the Nigerian Army and the country's main Shiite movement.
Any soldiers found guilty of misconduct or human rights abuses will face a court-martial.
Amnesty International says Mohammed may be responsible for mass executions.
President Buhari has ordered that 20 retired and serving military officials be investigated for corruption.
At least 300 Shiites were killed in clashes with the army in Zaria, northern Nigeria.
The Shiite movement claims dozens of its members were killed by soldiers on Saturday.
The army has a December deadline to reclaim all Boko Haram-held territory.
The second assault on the city in a week comes as regional powers rally against the terror group.