The Vatican announced the resignation of the bishop of Rancagua, 78-year-old Alejandro Goic Karmelic and the bishop of Talca, Horacio del Carmen Valenzuela Abarca, 64.
Several senior members of Chile's Catholic Church are accused by victims of ignoring and covering up child abuse by paedophile priest Fernando Karadima during the 1980s and 1990s.
The entire Chilean delegation of bishops tendered its resignation to the pope in May after a series of meetings at the Vatican.
Earlier this month, Francis accepted the resignation of three Chilean bishops, including the controversial Juan Barros who Karadima's victims accuse of covering up wrongdoing.
The pontiff himself became mired in the scandal when, during a trip to Chile in January, he defended Barros. However the pope later apologised to Karadima's victims and said he had made "grave mistakes".
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