The installation of Juan Barros earlier this year as the Bishop of Osorno, in southern Chile, was heavily protested by those accusing him of having protected Fernando Karadima, a priest the Vatican in 2011 found guilty of child sex abuse, committed in the 1980s.
Barros has denied the allegations against him. But 51 members of the Chilean Congress sent a letter protesting his appointment to the Vatican.
Parishioners in Osorno, some of whom opposed the nomination of Barros, had asked the Vatican for a message.
"Think - with your head - and do not be swayed by the unfounded allegations of lefties," Pope Francis said in footage broadcast Saturday by the Chilean TV channel Mega.
The Argentine pontiff got blunter: "Osorno is suffering from stupidity, and for not opening its heart to what God says. And for letting itself get carried away by the garbage everybody says," he added.
The pope's statements come three weeks after the archbishop of Santiago, Ricardo Ezzati, asked for forgiveness during a homily after revelations, in leaked emails, that the Chilean Church officials had worked to cover up the Karadima case.
Last week, the pope addressed the child sexual abuse issue on a visit to the United States.
Around 6,400 Catholic clergy have been accused of abusing minors in the United States alone, between 1950 and 1980, though campaigners fear the number could be higher.
Activists welcomed what they called a long-awaited admission by Francis that the Church had covered up abuse. But they said only actions, not words, could make a real difference.
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