In a report released today, the London-based rights group accused Nigeria's army of showing "little regard for the rule of law or human rights" in its fight against the rebels.
The human rights body listed some of the violations committed by both sides to include; enforced disappearance, torture, extra judicial executions, torching of homes and detention without trials.
But Nigeria's Minister of Foreign Affairs Ambassador Olugbenga Ashiru dismissed the allegation of human rights abuses levelled by the group.
"The security forces have been very restrained in their response to the complex challenge posed by the insurgents, many of who remained faceless and brutal in their tactics. Members of Nigeria security forces had fallen victims to the Boko Haram sect in the course of carrying out their lawful duties," the minister told PTI.
He urged Amnesty to be more circumspect, nuanced and balanced in their assessment of the situation in the country.
Presenting the report titled "Nigeria: Trapped in the Circle of Violence", in the country's capital Abuja, the Secretary General of the human rights body, Salil Shetty said: "People are living in climate of fear and insecurity, vulnerable to attack from Boko Haram and facing human rights violations at the hands of the very state security forces which should be protecting them."
"Hundreds of people accused of having links with Boko Haram have been arbitrarily detained by a combination of the Joint Task Force, JTF, a combined forces group commissioned by the President to restore law and order in areas affected by Boko Haram" the report stated.
It also stated that many have remained in detention facility for lengthy periods without charge or trial, without proper notification of family members, without being brought before any judicial authority, and without access to lawyers or the outside world.
It further stated that a significant number of these people have been extra-judicially executed.
Meanwhile, a person who identified himself as a member of Boko Haram, Abu Mohammed Ibn Abdulaziz said the group is ready to hold a peace talk with the Nigerian government in Saudi Arabia in order to end its insurgency which has claimed hundreds of lives.
He gave as condition for the negotiation, the involvement of a former military dictator General Muhammadu Buhari.
According to him, the group is not actually challenging the Nigerian state but fighting against the high handedness with which the military has cracked down on its members.
Boko Haram wants to install an Islamic caliphate in northern Nigeria though the region has a large number of Christians who are in the minority.
In the southern part of the country where the Christians are in majority, the sect has not been able to establish its presence.