The Vatican said the latest to leave their posts were the bishops of San Bartolome de Chillan and of San Felipe.
No reasons were given for the resignations but the Chillan diocese was one of four raided by Chilean authorities last week in investigations of clergy sexual abuse of minors and the hierarchy's alleged cover-ups.
Chile's bishops earlier this year offered to resign en masse, responding to Francis' belated efforts to clean house there.
Francis had underestimated the pervasiveness of paedophile priests and other church abuse in Chile, but later acknowledged errors in his judgment.
He met on Friday at the Vatican with the archbishop of Concepcion, another of the raided dioceses.
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