The corpses, some mere skeletons, were found in a disused fuel tank at a camp of former fighters of the mostly Muslim Seleka rebel group whose coup a year ago sparked the country's descent into chaos.
The bodies "were found in different places in the tank, which suggests that the people were thrown in there alive and struggled to get out," Ghislain Grezenguet, lead prosecutor in the capital Bangui, told AFP.
They were found by international peacekeepers whose suspicions were aroused by the nauseating stench coming from the site, he said.
The camp commander, Aboubakar Mahamat, told AFP that he had "said everything to the investigators."
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Killings and pillaging by ex-Seleka rebels following the coup led to the formation of mainly Christian militias, whose attacks in recent weeks have led many minority Muslims to flee the country.
Clashes broke out today at a camp for displaced Muslims in Bangui.
Suspected members of the mainly-Christian anti-Balaka militias opened fire and hurled a grenade into the camp, a humanitarian source said, leaving one dead and two injured among the displaced.