The human rights group has called on the international community to push for an independent investigation into alleged abuses after a bloody three months which have left more than 1,500 dead.
In particular, Amnesty alleged that hundreds of suspected militants were summarily executed after escaping from a detention facility at the Giwa barracks in the northeast city of Maiduguri on March 14.
Defence spokesman Chris Olukolade said the military would look closely at Amnesty's claims but so far had not received the group's report.
He told AFP: "It's strange that despite all our efforts to ensure that we observe every detail of human rights requirement that any organisation is still desperate to compare us with terrorists.
"It is unfortunate. We feel the motive is suspect….
"But we know that in our own case, we have continued to try our best that human rights are not abused and we will continue to go by the best standard in our operations."
Nigeria's military has been under pressure over its tactics to counter the insurgency by Boko Haram, with criticism that its conventional strategy was ineffective against guerrilla fighters.
The top brass, however, maintain that the increased violence is a reaction against a troop surge in the northeast, tighter security plus the discovery of arms dumps and destruction of makeshift camps.
Amnesty and other human rights monitors had previously accused the military of holding detainees in atrocious conditions at the Giwa camp, saying prisoners faced ill-treatment, torture and even death.
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