Bishop Valerio Breda's says the case has brought "shame and dishonor" on the church.
His open letter was made public on Thursday.
An 83-year-old priest in the northeast state of Alagoas is accused of sexually abusing at least three boys as young as 12.
He is under house arrest and prosecutors are weighing charges.
Breda calls on worshippers to "not have fear of the truth, even if it is painful."
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