Amnesty International said the country's military used live ammunition and deadly force against pro-Biafra protestors who were campaigning for independence from Nigeria.
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 Onitsha, in the two days surrounding Biafra Remembrance Day in May 2016.
"This reckless and trigger-happy approach to crowd control has caused at least 150 deaths, and we fear the actual total might be far higher" said Makmid Kamara, Amnesty's interim director for Nigeria.
Other victims detailed in the report include a 26-year-old man who was shot in Nkpor, but hid in a gutter, still alive. He said when soldiers found him, they poured acid over him, and told him he would die slowly.
Another woman said she had been speaking to her husband on a mobile phone when he told her he had been shot in the abdomen. He was calling from a military vehicle, she said, and she heard gunshots. She later found his body in a morgue with two more wounds in his chest, leading her to believe he had been executed after the call.
The human rights organisation said pro-Biafra protests had been "large peaceful" despite occasional incidents of protester throwing stones and burning tyres - and one occasion when someone shot at police.
"Regardless, these acts of violence and disorder did not justify the level of force used against the whole assembly."
But army spokesman Sani Usman that "the military and other security agencies exercised maximum restraints despite the flurry of provocative and unjustifiable violence".
A Biafran state
In the past year there have been a series of protests by supporters of the Indigenous People of Biafra.
The movement wants to create an independent state - Biafra - in the southeast of Nigeria, home to the Igbo people.
A previous attempt to establish a state triggered the Nigerian civil war almost 50 years ago, in the aftermath of Nigeria's 1966 coup.
Unaddressed grievances from 1966 lie at the heart of the Biafra movement's resurgence.
Many Igbos feel that Nigeria is still punishing them for their previous attempt at secession.