The United Nations report says the civilian deaths represented a 324% rise over the last three months of 2021.
It also spotlighted what it terms the failure of Mali's military junta to limit human rights abuses or stop groups linked to al Qaeda and Islamic State from carrying out campaigns of violence.
"Malian Armed Forces, supported on certain occasions by foreign military elements, increased military operations to combat terrorism ... some of which sometimes ended in serious allegations of violations of human rights," the U.N.'s Malian mission, known as MINUSMA, said in the report.
MINUSMA documented 320 human rights violations by the Malian military in the January-March period, compared with 31 in October, November, and December.
The most notable case was in the town of Moura, where witnesses and rights groups say the Malian army accompanied by white fighters killed scores of civilians they suspected of being militants. read more
"In addition to summary executions, security forces also allegedly raped, looted, arrested and arbitrarily detained many civilians during the military operation," MINUSMA said.
The surge in civilian deaths, known in military terms as "collateral damage," came as the Sahel nation severed ties with former colonial power France, and Bamako hired Russian private military company Wagner Group\to help defeat militants who have carried out attacks in Mali's center and north for nearly a decade.
Mali has been hit by violence since 2012 when jihadists took over the north. France beat them back, but by 2015 they had regrouped and unleashed a wave of attacks in the centre. They have since spread into Niger and Burkina Faso, raising concerns of regional instability.
Mali's military, which took power in a 2020 coup, did not respond to requests for comment. Wagner Group could not be reached.