Primarily nomadic herders, the Fulani are often stigmatised across the Sahel, accused of collaborating with armed Islamist groups and providing the bulk of their recruits.
Mali's army and the Wagner paramilitary group "appear to have executed at least 12 Fulani men and forcibly disappeared at least 81 others since January", HRW said.
It said it had credible reports, corroborated by the United Nations, that 65 of the missing from a village in the western Kayes region had been executed in April.
"The Malian soldiers and Wagner group fighters accuse the Fulani community of collaborating with Islamist armed groups fighting to control parts of the country," HRW said.
On March 30, the Malian military and Wagner fighters entered Belidanedji in the central Segou region "and summarily executed at least six Fulani civilians who were fleeing or hiding," HRW said, citing witnesses.
"They shot my friend in the chest in front of me," it quoted a 47-year-old man as saying.
"When the soldiers left, we recovered five bodies and evacuated an injured man, but he later died in the hospital."
HRW said the deaths and disappearances were carried out "in the context of counterinsurgency operations across several regions of the country".
The army is fighting the the Al-Qaeda-affiliated Group for the Support of Islam and Muslims, known by its Arabic acronym JNIM.
The executions and abductions were carried out in the regions of Douentza, Kayes, Segou and Timbuktu and also included house burnings and torture, HRW said.
HRW interviewed 29 people with knowledge of the incidents by phone between February and May, including 16 witnesses.
The rights group called on the African Union to pressure Mali's junta to carry out an investigation and prosecute those responsible.
"Senior Malian and Russian officials should recognize that they can be held responsible for the crimes committed by their soldiers and fighters", said Ilaria Allegrozzi, HRW senior Sahel researcher.
The Wagner group announced its departure from Mali in June after being involved in the country's anti-jihadist campaign since 2021.
It has been replaced by Africa Corps, another paramilitary group with links to the Kremlin.
Mali is ruled by a junta that came to power following two successive coups in 2020 and 2021.
HRW said it had sent its findings and questions to the country's justice and defence ministers but had received no response.
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