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 human rights organisation said in a report seen by AFP on Thursday.
HRW pointed the finger at GSIM fighters for the massacre on the Timbuktu ferry on Mali's Niger River on September 7, which left at least 120 people dead according to witness testimonies collected by the organisation.
Malian soldiers and fighters apparently from the Russian mercenary group 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 is based on telephone interviews with 40 people conducted in August and September.
HRW senior Sahel researcher Ilaria Allegrozzi said that the figures recorded only related to five cases specifically investigated by the organisation, and that the number of civilians killed during that period in Mali could be much higher.
The country, ruled by a military junta since 2020, has been locked in the grip of jihadism and a deep multidimensional crisis since 2012.
HRW said it had sent its findings to Malian authorities but had not received a response.
AFP was unable to obtain any reaction.
"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," said Allegrozzi.
The organisation called on Mali's transitional military authorities to, with the support of international rights experts, "urgently conduct credible and impartial investigations into the alleged abuses, and hold those responsible to account."
- Heightened tensions -
Since the end of August, northern Mali has seen a resumption of hostilities by predominantly Tuareg separatist armed groups and an intensification of jihadist attacks against the Malian army.
Human rights organisations and the UN peacekeeping mission, MINUSMA, have on numerous occasions accused the army of rights abuses.
Members of Wagner have also been criticised since their arrival in the country.
The authorities say they monitor respect for human rights and carry out investigations where necessary, but the results are never made public.
In June, the Malian junta demanded that the peacekeepers leave "without delay," forcing an unprecedented hasty withdrawal, due to be completed by year's end.
The military rulers proclaimed the UN mission a "failure" and denounced its alleged "instrumentalisation" of the human rights issue.
MINUSMA's withdrawal has exacerbated rivalries between all the armed actors vying for control of the terrain -- including separatists, jihadists and the regular army.
HRW said one of the incidents it focused on was the reported abuses committed during an army operation in the western village of Trabakoro in search of GSIM fighters.
Witnesses interviewed by the organisation said that on April 22, two military helicopters opened fire on the village, followed by soldiers going door-to-door shooting at people inside their houses and outside as they fled.
They said soldiers killed 18 people, including 14 children and four women.
"The soldiers killed women and children whom they took to be women and children of jihadists," a resident told HRW.
In a separate incident on August 6, Malian soldiers accompanied by several "white" fighters in military uniforms, seemingly members of Wagner, carried out an operation in the northern village of Sambani, where the GSIM is known to operate, HRW said.
"Authorities arrested 16 men and a boy, whose bodies were later found outside the village," the organisation said.
"All the victims appeared to have been shot in the head and tortured," a man who was at the scene told HRW.
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