Charles Sikubwabo served as Bourgmestre (mayor) of Gishyita in the Kibuye préfecture during the Rwandan genocide in 1994. According to an indictment dated 29 April 1996, Sikubwabo allegedly conspired with convicted génocidaires, Clément Kayishema, Mikaeli Muhimana and Obed Ruzindana to kill the Tutsi population in Kibuye.
Charles Sikubwabo is charged by way of his individual and superior responsibility for the massacres at Mubuga Church and massacres in the area of Bisesero. In each massacre, the indictment claims that thousands of predominantly Tutsi men, women and children were killed, with Sikubwabo directing members of the communal police and Interahamwe to attack the church and other areas where refugees had gathered. Charles Sikubwabo is also charged with participating in the killings himself. He is charged with genocide, murder, extermination and other inhumane acts (crimes against humanity) as well as war crimes.
After the genocide was halted, Sikubwabo fled Rwanda, with the indictment suggesting that he may be residing in the DRC. Charles Sikubwabo remains at large, with the International Criminal Tribunal for Rwanda (ICTR) seeking to complete its work in 2010.