The Nigerian military has been accused of arbitrary arrests and executions of people suspected of being members of the Islamist group.
The rights group claimed that nine senior commanders had overseen torture and abuses that led to some 8,000 deaths.
Nigeria has a patchy human rights record and has mistakenly bombed displaced civilians.
Colonel Samaila Inusa was found dead on Tuesday after being abducted in Kaduna two days earlier.
Amnesty International says Mohammed may be responsible for mass executions.
The U.S. has also authorized the deployment of 300 troops to Cameroon to fight the insurgents
The Nigerian jihadist group are reported to have killed 2,000 since the beginning of the year.