Amnesty International said the military used live ammunition and deadly force against pro-Biafra protesters who were campaigning for an independent state in the south-east.
Nigeria's police denies allegations that it used unnecessary force.
The country's army said Amnesty was trying to tarnish its reputation.
Amnesty's report is based on interviews with almost 200 people, alongside more than 100 photographs and 87 videos.
Among the allegations contained in the report are what Amnesty called "extrajudicial executions", when 60 people were shot and killed in south-eastern Onitsha city, in the two days surrounding Biafra Remembrance Day in May 2016.
