Amnesty International said the Nigerian military fired live ammunition to disperse members of the Indigenous People of Biafra (IPOB) group between August 2015 and August 2016.
"This reckless and trigger-happy approach to crowd control has caused at least 150 deaths," said Makmid Kamara, interim director of Amnesty International Nigeria, who called on authorities to launch an investigation.
The 60-page report was based on interviews with 193 people, 87 videos and 122 photographs from the period. It said troops and the police used "arbitrary, abusive and excessive force to disrupt gatherings."
It also found evidence of mass extrajudicial executions by security forces, including at least 60 people shot dead in the space of two days in connection with events to mark Biafra Remembrance Day.
The report is the latest in a string of accusations leveled at the army by Amnesty. In 2015, it said over 8,000 people died in detention during a crackdown on the northern Islamist group Boko Haram.
IPOB reignites Biafran question
Calls for succession from Africa's most populous nation flared up again last year after IPOB leader Nnamdi Kanu was detained on charges of criminal conspiracy.
The Biafra separatist rebellion first flared in the west African country during the 1967-1970 civil war that saw around 1 million people killed.
IPOB emerged in 2012 and campaigns for an independent Biafran state.
Army denies wrongdoing
Army spokesman Sani Usman said Amnesty's report was "aimed to tarnish the security forces' reputation," adding that Biafra separatists had behaved violently, killing five police officers at a protest in May and attacking both military and police vehicles.
"The military and other security agencies exercised maximum restraints despite the flurry of provocative and unjustifiable violence," he said.
"We don't attack people who are demonstrating, which every Nigerian has a right to do," he said.
Nigeria Police Force spokesman Don Awunah said officers "always abide by the law" and adhere to best practices.