The report said five senior Nigerian officers who served as commanders in the northeast against Boko Haram may be responsible for extra-judicial murder, torture and other crimes against alleged Islamist suspects.
It also said top service chiefs should be investigated for possible command responsibility due to acts committed by their subordinates.
"The officers mentioned in the report have no reason, whatsoever, to indulge in the allegation made against them," defence spokesperson Chris Olukolade said in a statement.
"It is unfortunate that the organisation just went out to gather names of specified senior officers, in a calculated attempt to rubbish their reputation as well as the image of the military," he added.
Amnesty said the allegations made in the 133-page report were based on hundreds of interviews, including with military sources, and using leaked defence ministry documents.
But Olukolade charged the group with using evidence provided by "certain disgruntled elements or faceless collaborators who have axe to grind with the system".
Nigeria's military has several times previously accused Amnesty of having hidden motives, without providing details or evidence regarding such claims.
The rights group has been fiercely critical of Nigeria, including over alleged abuses in the counter-insurgency effort in the northeast and for its policies in the oil-producing Niger Delta region in the south.
Olukolade said past allegations made by Amnesty "had been thoroughly responded to and cleared in the public and officially".
But that claim did not appear consistent with recent history, as multiple reports of human rights abuses by the military have not been subject to an official probe.
Amnesty said it communicated extensively with the defence ministry before releasing its latest report.
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