At least 180 bodies have been found in common graves in Djibo, a town in the north of Burkina Faso and Human Rights Watch says the killings were likely carried out by government forces.
Available evidence suggests government forces were involved in mass extrajudicial executions, the report released on Wednesday stated.
The group called for the Burkina Faso government to hold those responsible to account and the latter has promised to investigate the matter, reported.
The Minister of Defence, Mr Moumina Cheriff Sy, said the killings could have been committed by Terror groups using stolen army uniforms and logistical equipment.
It is difficult for the population to distinguish between armed terrorist groups and the defence and security forces,” he said.
Burkina Faso has been battling militant groups with links to al Qaeda and Islamic State since 2017. Hundreds of civilians have been killed and almost a million displaced by the conflict, which is also affecting its neighbours, Niger and Mali.
Despite promises to investigate and prosecute previous reports of rights abuses, rights groups say the government had been done.
Concerns over increased reports of abuses by soldiers prompted European Union and Sahel leaders to warn during a security summit on June 30 that any of their troops found guilty of human rights abuses would be punished severely.
The Human Rights Watch report said the killings in Djibo likely took place between November, 2019 and June, 2020.
Residents who saw the bodies told Human Rights Watch that the dead were all men.
It said the bodies were left in groups along major roadways, under bridges.