HRW said the abuses had been committed since late 2022 "during military operations in response to the presence of Islamist armed groups" in several towns in central Mali.
The international rights group also denounced cases of torture of detainees, destruction and looting of civilian property.
"Malian armed forces and foreign fighters apparently from the Russia-linked Wagner Group have summarily executed and forcibly disappeared several dozen civilians in Mali's central region," HRW said.
With the decade-old MINUSMA mission in Mali due to leave the landlocked West African country by the end of the year, the human rights NGO is urging the African Union and the Economic Community of West African States (ECOWAS) to press for an end to abuses and hold the Malian authorities to account.
Mali which is run by a military junta, has since 2012 been battling a jihadist insurgency that has spread to Burkina Faso and Niger, killing and displacing thousands of people.
The damning HRW report follows one it published earlier this month which denounced widespread killing, rape and looting in northeast Mali this year.
For the new report, Human Rights Watch said it had interviewed 40 people by telephone including 20 "witnesses of abuses, three family members of victims, two community leaders, five Malian civil society activists".
They reported the involvement of armed, non-French-speaking foreigners, describing them as "white", "Russian" or "belonging to Wagner".
One was recorded saying that a large number of "white" foreign fighters in uniform carried out a February 3 assault on the village of Seguela, which resulted in beatings, looting, and the arrest of 17 men with eight bodies later found at the scene.
In another attack, a 28-year-old witness said low-flying military helicopters had opened fire on the village of Ouenkoro in March
"People fled in all directions... I took my motorbike and rode as fast as I could," he said.
Responding to the HRW report, the Malian government said it was not aware of any human rights violations, but that the public prosecutor "has opened a judicial investigation for war crimes and crimes against humanity".
Since taking power in 2020, the ruling junta in Bamako has aligned politically and militarily with Russia and broken ties with traditional ally France.
The UN accused the Malian army and foreign fighters in May of murdering 500 people during an anti-jihadist operation, which the junta denied.
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