Its researchers met with senior government officials, including the ministers for police affairs, justice and the interior, and the defense headquarters representative, the rights group said.
Amnesty International also acknowledged the challenges faced by under-resourced police in the face of militant activity, and said the attacks by Boko Haram targeting civilians "may constitute crimes against humanity."
Over the past three years, Boko Haram has waged a violent campaign of bombings of Christian churches that have killed hundreds and wounded many more. There have been fewer attacks by Christian militant groups.
Nigeria has almost equal numbers of Christian and Muslims, with the south predominantly Christian.
Boko Haram and other Muslim groups claim the north has been starved of resources and marginalized by the government of President Goodluck Jonathan, a Christian.