The claim came as concerns rose over alleged abuses during counter-terror operations in the African country where extremists linked to al Qaida and the Islamic State group have carried out attacks.
Mali's government confirmed the existence of three graves discovered by residents about four miles away from the village of Nantaka and said it would investigate.
Soldiers detained several men on June 13 and released all but 25 ethnic Fulani, according to a resident who spoke on condition of anonymity out of fear for his security.
The soldiers who came to Nantaka buried the 25 men after killing them, said Ibrahim Thiokari of the Fulani association Tabital Pulaku.
The West African nation's defence minister, Tiena Coulibaly, acknowledged that residents were blaming members of the armed forces.
The army chief of staff was visiting the area on Tuesday.
"The minister reiterates his determination and strong will to fight against impunity and to engage the Malian army in the strict respect of the convention of human rights and international humanitarian rights in the conduct of operations," the minister's statement said.
Human rights groups have expressed concern about increasing allegations against Mali's armed forces as they carry out counter-terrorism operations in the Mopti region, where the Fulani are the majority and some have been recruited by extremist groups.
The vast majority of civilians reported killed in the operations have been Fulani.
"We welcome the investigations. However, those promises should not be empty.
"The government has to follow up with the investigations and ensure those involved are held to account, and that the family members know about it," said Corinne Dufka, associate director of West Africa for Human Rights Watch.
