Ramsey County Attorney John Choi on Friday criminally charged the Archdiocese of St. Paul and Minneapolis for its "role in failing to protect children and contribution to the unspeakable harm" done to three sexual abuse victims of former priest Curtis Wehmeyer.

Explore the full investigation Clergy abuse, cover-up and crisis in the Twin Cities Catholic church

The charges place responsibility for the abuse of those children not just on Wehmeyer "but the archdiocese as well," Choi told reporters as he announced the charges.

The six counts qualify as gross misdemeanors and could lead to fines against the archdiocese. Prosecutors "don't have sufficient evidence" to charge any church official at this point, he added.

This appears to be only the second time an American archdiocese has been indicted as an institution amid clergy abuse allegations. In 2003, the Archdiocese of Cincinnati was found guilty of failing to report clergy sexual abuse and was fined $10,000.

Choi said the Twin Cities investigation remains ongoing and "robust" and that new facts that support the allegations in the charges today have been uncovered.

Church officials time and time again turned a blind eye in the name of protecting priests at the expense of protecting children, Choi said.

Former priest Curtis Wehmeyer Minnesota Department of Corrections

"The facts we have gathered cannot be ignored, they cannot be dismissed, and are frankly appalling, especially when viewed in their entirety," Choi said. "The allegations reveal a disturbing way in which this organization said it protected children when in reality it did not."

Choi called the archdiocese's monitoring program for abusive priests "a sham," adding, "We were falsely led to believe that the leadership structure of the archdiocese had an effective program in place" for monitoring abusive priests.

Auxiliary Bishop Lee Piche spoke to a crowd from the steps of the state Capitol before leading a rosary procession in May 2012. Alex Kolyer for MPR News

Choi said that in 2010, a priest told Auxiliary Bishop Lee Piche that Wehmeyer had been on a camping trip with one of the boys who would later be identified as one of his victims and that Wehmeyer slept in the same bed with the boy, and that when asked of this, Piche said Wehmeyer "had many skeletons in his closet."

The Ramsey County Attorney's Office has also filed a civil motion that would force the archdiocese to stop the alleged illegal behavior. It asks the court to require the archdiocese to fix the conditions that led to the problems, a county attorney's office spokesman said.

Archdiocese officials late Friday afternoon said they'll continue to cooperate with law enforcement and the courts.

"I want to state clearly that we deeply regret the abuse that was suffered by the victims of Curtis Wehmeyer," Auxiliary Bishop Andrew Cozzens told reporters Friday afternoon. Cozzens and Timothy O'Malley, director of ministerial standards and safe environment for the archdiocese, appeared briefly outside the chancery to speak to reporters. Archbishop John Nienstedt did not join them and has not issued a statement on the charges.

Auxiliary bishop Andrew Cozzens, left, and Tim O'Malley, director of ministerial standards and safe environment for the archdiocese, spoke outside the Chancery about the criminal charges announced today against the church Friday. Jennifer Simonson | MPR News

The archdiocese shares the police and prosecutors' commitment "to prevent the kind of harm caused in the Wehmeyer case from ever happening again," added O'Malley.

St. Paul Police Chief Tom Smith asked anyone else with information about clergy misconduct to come forward as well.

"This case is not about religion. It's about allegations of misconduct and crimes that were committed," Smith said. "These types of allegations are always disturbing, especially when it involves people in positions of authority and trust."

Advocates for people abused by clergy called the charges against the archdiocese a good first step.

"If real justice is going to be done, and if the full truth is going to be exposed, and if cover ups are going to be deterred, more people who saw, suspected or suffered crimes and cover ups in the Twin Cities have to find some courage and pick up the telephone," said David Clohessy, executive director of the Survivors Network for those Abused by Priests.

Clohessy said he hopes Choi's continued active investigation of the archdiocese will result in criminal charges against individual archdiocese officials.

As church bells rang outside the Chancery Friday evening, Frank Meuers said it was "high time" church officials face criminal charges.

Frank Meuers, director of the southern Minnesota chapter of Survivors Network of those Abused by Priests, spoke to the media about criminal charges against the Archdiocese of Saint Paul and Minneapolis Friday. Jennifer Simonson | MPR News

Meuers, a local SNAP leader, said he's a victim of clergy sexual abuse himself. He has been pushing for criminal charges since the allegations against the archdiocese surfaced over two years ago.

"What we always have asked for is accountability," he said. "And there is no reason to believe that you wouldn't get that from officials in any organization.

"You would especially predict that they would be forthcoming in a religious organization."

A long and complicated investigation

The charges against the institution mark a milestone in a 20-month investigation by St. Paul police and Ramsey County prosecutors into the handling of clergy sex abuse by archdiocese officials.

It began in October 2013 when St. Paul police opened an investigation into the handling of allegations of child sexual abuse by Wehmeyer, who was arrested in 2012 and pleaded guilty to sexually abusing two sons of a parish employee and possessing child pornography.

He was removed from the priesthood in March 2015 and is serving a five-year prison sentence. He's also facing prosecution in Chippewa County, Wis., for sexually assaulting a teenage boy.

The police review of the case was prompted by an MPR News report that showed several church officials did not immediately report allegations about Wehmeyer to police.

Three months later, in January 2014, Choi held a news conference to announce that no charges would be filed against any church officials for their handling of the Wehmeyer case.

Within hours, MPR News obtained documents that provided further evidence of Nienstedt's knowledge of the Wehmeyer allegations. Those documents led Choi and police to reopen the case.

Archbishop John Nienstedt celebrated Holy Thursday Mass in April 2015 at the Cathedral of St. Paul. Jennifer Simonson | MPR News

Over the past year, the investigation expanded to include thousands of documents from lawsuits, news reports and other sources that detailed how church officials responded to allegations of clergy sex abuse.

Throughout that time, Choi has said little about the investigation and has faced criticism from victims and Ramsey County residents who said he wasn't being aggressive enough in holding church officials accountable to the law.

Attorney Jeff Anderson, who has represented victims of clergy abuse in court for decades, said the charges unveiled Friday are unprecedented and bold.

"It is a stinging complaint against the corporate culture and top officials that made the conscious choices to protect Wehmeyer and others," Anderson said. "That will send a message of accountability that is both powerful and real."

Among the findings in the court documents:

March 2012: Piche writes memo to Nienstedt saying Wehmeyer is paranoid and has bought a gun, and that any intervention should be handled carefully. Nienstedt responds with a handwritten note: "[T]his sounds serious. What do we do next? I go there for Mass on April 14."

May 2012: Meeting with Nienstedt met with Wehmeyer at Nienstedt's residence. Wehmeyer "flatly rejected" claims he had abused alcohol, said he was overwhelmed, said he was leaving for a weeklong vacation, and Nienstedt said he would follow up with Wehmeyer when Wehmeyer returned from vacation.

June 2012: Nienstedt writes a memo to Piche and Laird saying "he had just gotten a message from Wehmeyer about joining him and his therapist for a session later in June ... Nienstedt ended the June 6 memorandum: 'All in all, I think we are making some progress here.'"

March 2015: During a call from the Lino Lakes Correctional Facility where Wehmeyer is incarcerated, Wehmeyer said at the time of his appointment Nienstedt knew a lot about him but chose not to be as concerned as he should have been.

Wehmeyer said Nienstedt was aware he had been sent to St. Luke's and had drinking problems.

Wehmeyer said he asked the archbishop a couple of times, 'Are you aware of my past? Are you aware of my record?' Wehmeyer said that Nienstedt brushed it off and replied, 'I don't have time to look into that stuff.'"

Documents: Archdiocese criminally charged

MPR News reporters Riham Feshir and Laura Yuen contributed to this report.