ROME – Pope Francis has accepted the resignation of a controversial Chilean bishop accused of covering up clerical sexual abuse, making it the first such accepted resignation since all the country’s bishops offered to step down in May.

The pontiff had appointed Bishop Juan Barros to the southern diocese of Osorno in 2015, causing uproar both among the locals and the victims of the country’s most infamous pedophile priest.

The Vatican announced Francis’s decision on Monday, and said Bishop Jorge Enrique Concha Cayuqueo, an auxiliary bishop from the capital Santiago, would serve as apostolic administrator of the diocese.

Two other bishops also had their resignations accepted: Archbishop Cristián Caro Cordero of Puerto Montt and Bishop Gonzalo Duarte García de Cortázar of Valparaíso.

Barros was only 61; the other two bishops were 75, the mandatory retirement age for bishops in the Church.

The removals come ahead of a pastoral visit by two papal investigators to Osorno to “advance the process of reparation and healing.”

Archbishop Charles Scicluna of Malta, a former official of the Vatican’s Congregation for the Doctrine of the Faith, and Spanish Monsignor Jordi Bertomeu, a current official of the congregation, will be in the diocese June 14-17, but will arrive in Chile on the 12th.

Since appointing Barros back in January 2015, the pontiff openly defended him on more than one occasion. For instance, in May of that year, when a former spokesman for the Chilean bishops’ conference was in Rome and attended the pope’s public weekly audience, Francis was recorded saying, with no prompting, that the local church had “lost its head,” allowing a group of politicians to judge a bishop “with no proof whatsoever.”

“Think with the head, don’t be led around by the nose by these leftists who are the ones who put this [opposition] together,” the pope is heard saying.

The “leftists” to whom Francis referred are presumably 51 members of Chile’s Congress, most from the Socialist government of President Michelle Bachelet, who had signed a petition opposing Barros’ nomination.

During his trip to Chile in January of this year, the pontiff is once again caught on video defending the controversial bishop – one of four bishops who were mentored by Father Fernando Karadima, found guilty by the Vatican in 2011 of sexually abusing minors.

“The day I’m presented with proof against Bishop Barros, I will see,” Francis told journalists as he arrived in Iquique, in northern Chile, to celebrate his last Mass on Chilean soil.

“There’s not a single proof against him, it’s all a calumny,” the pope said, prompting a response from Boston’s Cardinal Sean O’Malley, who heads the Vatican’s Commission for the Protection of Minors. It was “understandable,” the American said, that the pontiff’s language had caused “great pain.”

On the way back from the trip to Chile – which also took him to Peru for three days – Francis once again defended Barros, saying that after the bishop had taken possession of the diocese, the investigation into the allegations had “continued, but no evidence emerged … I cannot convict him, because I have no evidence; but I am also convinced that he is innocent.”

His words, once again, caused uproar, both among those who’d been abused by Karadima and in the diocese of Osorno.

Yet something happened to make the pope change his mind. Ten days after Francis got back to Rome, the Vatican announced he’d decided to send Scicluna and Bertomeu to Chile to look into the Barros situation.

The two clergymen went first to the United States, where one of Karadima’s victims lives, and then to Chile. In the end, they spoke to 64 people, producing a 2,300 page report which apparently led to Francis’s sending a letter to the Latin American country in which he wrote: “I have made serious errors of judgement and perception of the situation, especially due to lack of truthful and balanced information.”

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Soon after the pope got the report, three of Karadima’s survivors traveled to Rome as papal guests, two weeks after which all the Chilean bishops traveled to the Eternal City and presented their resignations en masse, putting their pastoral roles in the hands of the pope.

Last weekend, yet another group of people affected by Karadima – either because they were abused by him, or because they spent the past two decades helping his victims – met with Francis.

With both groups of survivors the pope had private, individual meetings, while he welcomed the bishops as a group, only holding private encounters with a handful of them.

Barros is one of four bishops who were formed by Karadima, though one of them, due to health reasons, no longer has a pastoral assignment. The other three are Bishop Tomislav Koljatic Maroevic, who’s in Linares, Bishop Horacio Valenzuela, who’s in Talca, and Bishop Andrés Arteaga, who’s gravely ill. They all served as the auxiliary Bishop of Santiago de Chile and Vice-Chancellor of the Universidad Católica de Chile.

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Most allegations against Barros come from charges of covering up for Karadima. Duarte, on the other hand, has been accused of sexually abusing young seminarians himself. Reports dating back to 2011 include allegations of abuses of a sexual nature, but also of power and conscience.

For instance, Mauricio Pulgar, a former seminarian of the seminary of San Rafael in Valparaiso, said that in 1992 he saw Duarte publicly slap another student because he wouldn’t kiss him on the lips.

In 2012 Pulgar presented charges of abuse and cover-up against Duarte and other priests, but nothing ever came of it. Asked by local paper El Mercurio, the Chilean bishops’ conference said there was “no on-going investigation against Duarte,” nor was there one in the past.

However, Father Javier Astaburuaga Ossa, one of nine priests who met Pope Francis in early June, sent a letter to the editor of the newspaper saying that in 2008, he had presented a series of documents on Duarte to the papal representative in the country.

The cleric also said that in April 2008, before going to the papal ambassador, he’d spoken with Cardinal Javier Errazuriz, a member of the pope’s council of cardinal advisors and who himself has been accused of covering up for Karadima.

“I know that the information I’m giving can come at a personal cost for me, but the pope invited us to speak with the truth and this is an issue that I spoke to him about during the last weekend.”

In addition to these bishops, there are several others who’ve been accused of covering up cases of clerical sexual abuse, including Cardinal Ricardo Ezzati of Santiago and Bishop Alejandro Goic, who until last week was the president of the Chilean Church’s National Commission for the Prevention of Abuses, and who recently acknowledged that he hadn’t moved with appropriate nimbleness in a case of abuse in his own diocese. Both are over 75, so they originally presented the pope with their resignation before travelling to Rome.

In the weeks since the bishops have been back in Chile, there have been several more scandals related to cases of clerical sexual abuse, on occasion putting names and faces to the accusations Francis made in a confidential document he handed the Chilean bishops.

In it, the pope says that replacing bishops is “necessary” but not sufficient, and also accuses Chile’s hierarchy of destroying evidence in cases of clerical sexual abuse, pressuring Church lawyers to minimize accusations, moving priests with credible accusations of abuse to other dioceses and of “grave negligence” in protecting children from pedophile priests.