According to locals, the women aged 60 and 65 were alleged to be witches and causing the deaths of several people in the area.
They were said to have been rounded up late Sunday in the South Kivu village of Nyamutiri.
Andre Byaduniya, the head of a civil society in the area, made the revelation.
Timothee Bakanirwa, an official in an adjoining region, said: “The police and the army could not intervene in time to save these two women.”
Nelly Adidja from the Association of Women in Media (AFEM) said 33 women had been killed in South Kivu last year for alleged sorcery.
“Many others (witches) have been chased out of their villages,” she said.