MINNEAPOLIS (WCCO/AP) — Archbishop John Nienstedt says he leaves with Archdiocese of St. Paul and Minneapolis with a clear conscience and asks for prayers for its future leaders.

The archbishop and Auxiliary Bishop Lee Anthony Piche resigned abruptly Monday days after prosecutors charged the archdiocese 10 days ago with having failed to protect children from a pedophile priest.

In a statement, posted to the archdiocese’s website, Nienstedt said he has submitted his resignation in order to give the archdiocese a “new beginning amidst the many challenges we face.” He went on to say that his leadership drew attention away from the church.

As WCCO has reported for the past three years, dozens of clergy members have been accused of sexual abuse. Nienstedt himself had even been accused of having inappropriate contact with a boy. He was cleared.

“This has been a painful process, a change in leadership offers us an opportunity for greater healing and the ability to move forward,” Bishop Andrew Cozzens said at a press conference Monday morning. “We will continue to do everything we can to create safe environments for all children.”

Cozzens indicated the Vatican was in on the shakeup at the Twin Cities archdiocese.

The Vatican said Pope Francis accepted the resignations of Nienstedt and Piche. They resigned under the code of canon law that allows bishops to resign before they retire because of illness or some other “grave” reason that makes them unfit for office.

The resignations came just days after Francis approved the creation of a new tribunal inside the Vatican to hear cases of bishops who failed to protect children from sexually abusive priests. Francis’ decision followed years of criticism that the Vatican had never held bishops accountable for having ignored warnings about abusive priests and simply moved them from parish to parish rather than report them to police or remove them from ministry.

Rev. Bernard Hebda, the coadjutor archbishop of Newark, New Jersey, has been named temporary administrator of the Twin Cities archdiocese.

In a statement released Monday, SNAP Outreach Director Barbara Dorris said she believes Nienstedt should be punished.

“Though he has resigned, we still believe Nienstedt should be punished for enabling a predator to hurt kids. We hope these Vatican panels will quickly take up the Nienstedt case so that cover-ups will be deterred and kids will be safer,” Dorris said in the statement.

Earlier this year, the archdiocese ended up filing for bankruptcy amid numerous child sex abuse cases. Just 10 days ago, Ramsey County filed criminal charges against the archdiocese for failing to protect children.

In a July 2014 interview, Nienstedt defended placing a problem priest in a St. Paul parish.

“I knew he was same-sex attracted, but I never imagined he would be attracted to young minors,” he said, speaking of Curtis Wehmeyer.

But the charges filed by Ramsey County showed that Nienstedt and Piche were repeatedly warned about Wehmeyer. The two were said to even overlook a 2010 report by another priest that Wehmeyer had been caught in bed with a child.

Jennifer Haselberger, a former top Nienstedt aide-turned-whistleblower, said says the Nienstedt and Piche resignations were inevitable.

“It’s something that had to happen for the good of the church for the good of the archdiocese,” she said. “And I am glad it happened now.”

The Rev. Michael Tegeder, a Minneapolis priest who frequently criticized Nienstedt and had called for his resignation for years, said Monday that Nienstedt would have been happier elsewhere.

“He came into this diocese without really any empathy. He’s been, since age 14, in an all-male seminary and church environment. He just doesn’t relate to normal people,” Tegeder said.

Nienstedt’s rigid stance on church teachings became well known in 2010, when he appeared in a DVD that was mailed to several hundred thousand Catholic families around the state. On the disc, he called for a public vote on a constitutional amendment to define marriage as between one man and one woman. Several days later, he denied communion to a group of college students because they were wearing rainbow-colored buttons in support of gay rights.

Nienstedt explained his conservatism, saying he believed spiritual leaders have a duty to talk about important issues even if some of their views might be unpopular.

“I believe that it’s important that if you’re going to be Catholic, that you have to be 100 percent Catholic,” Nienstedt said. “That you stand by the church, you believe what the church believes and you pass that on to your sons and daughters and your grandsons and granddaughters.”

Nienstedt has spent the last two years trying to the repair the archdiocese. He has offered apologies and said in numerous statements that he was confronting clergy sex abuse. Late last year the archdiocese agreed to work with victims’ attorneys on a new set of protocols to protect children.

On Monday, he said he felt privileged to serve as the archdiocese’s leader, and he thanked his supporters.

“I leave with a clear conscience, knowing that my team and I have put in place solid protocols to ensure the protection of minors and vulnerable adults,” he said. “I ask for continued prayers for the well-being of this archdiocese and its future leaders. I also ask for your continued prayers for me.”

While Nienstedt is no longer in charge, he is still a bishop and able to perform masses and other sacraments.

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