In Bamako, the foreign ministry said the Human Rights Watch report released last week took a "sensationalist and biased approach" and put the nation's army "on the same level as the armed Islamist groups".
The ministry listed "unfounded allegations, gratuitous affirmations, testimonials taken from a distance and slanted, erroneous conclusions".
It also again denied working with Russia's Wagner paramilitary company, without naming it.
HRW said Islamist armed groups and Malian soldiers killed at least 175 civilians, many of them children, between April and September, condemning the targeted killing of civilians as war crimes.
The Al-Qaeda-linked Support Group for Islam and Muslims (GSIM) was responsible for the deaths of at least 135 civilians in two attacks, the organisation said.
Malian soldiers and fighters apparently from Wagner killed 40 civilians in three operations between April and September, it said.
Bamako's junta leaders struck up a partnership with Wagner after French troops pulled out of Mali in 2022.
The HRW report was based on telephone interviews with 40 people conducted in August and September.
Mali, under a military junta since 2020, has been locked in the grip of jihadism and a deep multidimensional crisis since 2012.
"The Malian government has failed to take adequate measures to protect civilians in conflict affected areas," Human Rights Watch said.
"The targeted killing of civilians by Islamist armed groups and the Malian army are war crimes that should be thoroughly and impartially investigated."
Human rights organisations and the UN peacekeeping mission MINUSMA have on numerous occasions accused the army of rights abuses.
"The Malian Armed Forces carry out their role with strict respect for the rights of man and international humanitarian law," the ministry said.
The authorities say they monitor respect for human rights and investigate where necessary, but the results are never made public.
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