Mali's chief prosecutor Daniel Tessougue said all signs pointed to the bodies being those of 21 soldiers who disappeared in April 2012 after a failed counter-coup by "red beret" soldiers loyal to ousted President Amadou Toumani Toure, but the formal identification process would have to be finalised.
"We will add murder to the charges (against Sanogo). If we find there are signs of torture we will add that too," he told the Reuters news agency, adding that military uniforms and IDs had been found at the scene.
The prosecutor was referring to General Amadou Sanogo, who was arrested and charged with complicity in kidnapping last week. Sanogo led the March 2012 coup that plunged Mali into chaos.
Judicial sources said 21 bodies had been found in the village of Diago near the southern garrison town of Kati, about 30 km (19 miles) north of the capital Bamako.
Moktar Mariko, a lawyer representing families of the missing soldiers told DW's French for Africa service "we knew the bodies had to be buried somewhere."
Authorities told of grave "a long time ago"
Yacouba Coulibaly, a Diago resident, told Reuters "we saw authorities come and exhume the bodies." Coulibaly said they had informed the authorities a long time ago that there was a mass grave in the area.
A senior military source said authorities had been instructed to inspect the site by judge Yaya Karambe, who is presiding over Sanogo's case.
Several other soldiers were questioned in an investigation into last year's counter-coup and into the deaths of soldiers in a mutiny in September this year.
A security official told the AFP news agency that "identity cards founds in the mass grave seem to confirm that they were missing "red beret" soldiers."
Rights groups call for further investigations
The case against Sanogo and several other soldiers is part of efforts by President Ibrahim Boubacar Keita to assert civilian control over the army, accused by human rights groups of excessive violence and torture during a chaotic 18 months when rebels occupied northern Mali last year.
Corinne Dufka, senior West Africa researcher at Human Rights Watch said the Diago killings were far from being an isolated case.
"It is crucial that the momentum started by the "red beret" case be sustained by investigations into other recent abuses, including by Malian soldiers, armed Islamists and the Tuareg separatists," she said.
The rights group Amnesty International said in a press release it welcomed the efforts the Malian government was making towards restoring justice and rule of law. Amnesty Mali researcher Gaetan Mootoo said "More needs to be done to establish the truth of all grave human rights violations committed over the last two years."