"These allegations are mostly tendentious, unconnected and deliberate, with the aim of tarnishing the image of the Malian defence and security force," the junta-controlled government said in a document published late Thursday.
"Facts are presented on the basis of... witness accounts backed by no real evidence and often made under the threat of terrorist groups."
The International Federation for Human Rights (FIDH) published the report on Thursday listing an unprecedented increase this year in the number of attacks on civilians in central Mali.
"Community self-defense groups, jihadists insurgents... the Malian armed forces and their international partners in the Russian paramilitary group Wagner continue to commit grave crimes, fueling the cycle of violence," the report said.
"Attacks, summary executions, sexual violence: in central Mali the civilian population is in a living hell," it said.
The report also highlights "the impunity of those responsible" and "slowness of judicial proceedings."
The junta-issued document said the army operated "with strict respect for human rights and international humanitarian law" and any alleged violations were always followed by "diligent treatment" and investigations.
The use of Wagner's services was explained by stating the mercenaries' presence involves "Russian trainers and advisers" who have been in Bamako since 1960, according to the document, when "certain instructors" helped build the national army.
The Wagner Group has been widely condemned for actions in a number of African and other nations where crimes against humanity have been committed.
The government said it "totally rejects" the FIDH charges of persecution against the Peul community, which is often accused of supplying men for jihadist groups.
Bamako claimed the FIDH had ignored the "remarkable progress" the government has achieved against the jihadists, as well as efforts to stop impunity for crimes with changes underway in penal and military law, and a plan to set up a special court to handle gender crime.
The Malian Association for Human Rights (AMDH), which is a member of FIDH and worked with it on a report in 2018, issued a statement saying it "dissociates itself" with the latest report because of "serious failings" involving "impartiality, objectivity and loyalty".
Mali has since 2012 seen thousands killed and hundreds of thousands flee their homes, in an insurgency that has spread to neighboring Niger and Burkina Faso.