Los Angeles Archbishop José H. Gomez forwarded that recommendation to the Holy See.

“These decisions have been made out of deep concern for the healing and reconciliation of abuse victims and for the good of the Church’s mission,” Gomez wrote in a letter to church members, released at the same time as the Vatican announcement.

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For Francis and the scandal-shaken Catholic Church, the resignation marks just the latest in a series of alleged misconduct cases involving powerful figures within the faith. The string of cases highlights the difficulty the Vatican has faced in ending the scourge of clerical sexual abuse and in holding accountable those in the high ranks of the church.

The statement by the Archdiocese of Los Angeles on Wednesday laid out a timeline of events that spanned several decades, but it did not make clear what led to Salazar being publicly disciplined only now.

The archdiocese said the allegation was reported directly to law enforcement in 2002. Authorities then investigated and recommended prosecution. But the district attorney did not file charges.

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The statement said the archdiocese was first informed — “through a third party” — of the allegation against Salazar in 2005. Salazar denied the allegation and the archdiocese has not received any other accusations against him, according to the statement.

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An archdiocese spokeswoman said the allegation from the 1990s “involved a single individual with multiple incidents, including boundary violations.”

Cardinal Roger Mahony, then the archbishop of Los Angeles, referred the allegation to the powerful Vatican body that investigates abuse cases.

That office, known as the Congregation for the Doctrine of the Faith, investigated and “permitted Bishop Salazar to remain in ministry subject to certain precautionary conditions, which he has respected.”

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The Archdiocese of Los Angeles did not elaborate on those precautionary measures, and a spokeswoman referred questions about them to the Holy See. A Vatican spokesman declined to provide details.

Salazar continued to appear at events with minors, according to contemporaneous news articles and archdiocese news releases.

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Several weeks ago, according to a Los Angeles archdiocese spokeswoman, the Clergy Misconduct Oversight Board looked back into Salazar’s case after Gomez requested a “full review of all allegations of sexual misconduct involving minors,” as part of an update to a list of accused priests.

That board, chaired by a layperson, was created as one of the steps taken within the U.S. Catholic church after stories of clerical sex abuse first exploded in 2002.

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Kurt Martens, a professor of canon law at Catholic University, said it was difficult to determine whether church authorities had properly handled Salazar’s case, and that more transparency was necessary.

“Here you have an allegation sitting there since 2005, and yet it’s 2018, and some action was undertaken. I find that very weird,” Martens said. “Why couldn’t that happen earlier? And why was [Salazar] kept in ministry with some restrictions?”

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The Los Angeles archdiocese recently released an update to its list of accused priests, but Salazar was not mentioned in that document.

The archdiocese said that over the past decade there have been two cases of misconduct involving minors by Los Angeles priests, both of which were made public when the allegations were first received.

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“In the past two decades, we have put in place an effective system for reporting and investigating suspected abuse by priests and for removing offenders from ministry,” Gomez wrote in a Dec. 6 letter.

The Catholic Church has dealt this year not just with cases of predator priests, but with cases that expose the misdeeds of bishops and cardinals, who either failed to stop abusers or carried out abuses themselves. Scandals have played out in France, Chile, Australia, the United States and elsewhere, implicating members even of Pope Francis’s inner circle. Increasingly loud critics say Francis’s papacy has been damaged by the cases — and by the church’s struggle to hold prelates accountable.

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In February, the Vatican is hosting an unprecedented summit bringing together leading bishops from around the world to discuss the protection of minors and clerical sexual abuse. On Tuesday, summit organizers asked participating bishops to meet with abuse victims before coming to Rome as a way to “learn firsthand the suffering” of those survivors.

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Salazar, 69, was born in Costa Rica but attended high school, college and seminary in California. He was ordained as a priest in 1984 and subsequently served several parishes across Southern California. He was ordained as an auxiliary bishop in 2004.

During that ceremony, according to a story that appeared in the Los Angeles Times, Mahony referenced a series of flash points across the world, as well as the church’s crisis in dealing with priestly sexual abuse.

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“So, Bishop Alex, it is precisely those realities that our Lord Jesus Christ calls you to and sends you,” the newspaper quoted Mahony as saying.