Updated: 7:29 p.m. | Posted: 11:09 a.m.

Archbishop John Nienstedt, leader of the Archdiocese of St. Paul and Minneapolis, has voluntarily "stepped aside from all public ministry" while police investigate an allegation that he touched a boy on the buttocks in 2009.

"I must say that this allegation is absolutely and entirely false."

In doing so, Nienstedt becomes the first sitting U.S. bishop to voluntarily relinquish some of his duties because of a police investigation into alleged sexual misconduct, said the Rev. Thomas Doyle, a priest and canon lawyer who worked at the Vatican Embassy in Washington, D.C.

Nienstedt denied doing anything wrong.

"I must say that this allegation is absolutely and entirely false," the archbishop wrote in a letter posted on the archdiocese's website. "I have never once engaged in any inappropriate contact with a minor."

The St. Paul Police Department began its investigation at 2 p.m. Monday after the archdiocese encouraged a person within the church who is required by law to report allegations of abuse to contact authorities. In a statement this morning, archdiocese officials said they learned of the allegation from that person.

St. Paul Police Chief Tom Smith talked to reporters at a news conference Tuesday to discuss investigations into clergy abuse and allegations against Archbishop John Nienstedt. | Read the story Jennifer Simonson/MPR News

It is not clear why the person who reported the allegation did not first notify law-enforcement officials.

"The statute's intent is that the mandatory reporter report the incident to law enforcement," said Dennis Gerhardstein, spokesman for the Ramsey County Attorney office. "I have a call in to [the St. Paul Police Department] to find out who knew what and when."

• MPR News investigation: Archdiocese under scrutiny

This month, Nienstedt released a list of 30 priests who the archdiocese says have been credibly accused of sexually abusing children. Nienstedt also ordered a review of clergy personnel files to ensure no other abusers are in ministry.

The List: The Archdiocese of St. Paul and Minneapolis released the names of 30 priests who it says have credible accusations of child sexual abuse against them. It also released the names of four priests who it says should not have been included in a 2002 tally of offender priests. Photo illustration by Regina McCombs/MPR News

The actions came after an ongoing MPR News investigation found that church leaders — including Nienstedt — protected abusive priests during their tenures.

The MPR News investigation has revealed that church leaders:

• Failed to report to police the discovery of possible child pornography on a priest's computer.

• Gave special payments to offending priests.

• Failed to warn parishioners of a priest's sexual addiction and attraction to boys. That priest later sexually abused two minors.

In the wake of the MPR News reports, police in two states reopened child sexual abuse and child-pornography possession cases; the archdiocese's top deputy resigned and Nienstedt postponed a $160 million capital campaign.

Tuesday afternoon, St. Paul Police Chief Tom Smith said the archdiocese is not cooperating with an ongoing criminal investigation into clergy sexual abuse.

"As of right now, except for attorneys, and being told no in a specific instance on the investigations before the allegations today, we have not been successful," Smith said.

The Rev. Kevin McDonough served as the archbishop's deputy from 1991-2009. Getty Images/File 2007

• Related: Police: Archdiocese not cooperating with clergy abuse investigation

Smith said the former top church deputy, the Rev. Kevin McDonough, has refused to talk to police. Smith also expressed frustration at being unable to talk to archdiocese staff.

The accusations against Nienstedt involve a boy who is a minor, according to the archdiocese statement. Nienstedt, who learned of the allegations more than a week ago, said he does not know his accuser's identity.

"The single incident is alleged to have occurred in 2009 during a group photography session with the archbishop following a confirmation ceremony," archdiocese officials said in a statement.

Doyle, the canon lawyer, said he had a hard time believing that a bishop, "even he was sexually attracted to children would do something like this, particularly in the current local and national climate."

Only four sitting U.S. bishops in history have had confirmed sexual activity with minors, Doyle said.

Nienstedt also has served as bishop of the Diocese of New Ulm. Dan Rossini, a spokesman for the diocese, said no allegations of sexual misconduct were made against him there.

• Related: Nienstedt's tenure in the Twin Cities

Archbishop John Nienstedt celebrated Mass Sunday at Our Lady of Grace parish in Edina, Minn. He told parishioners and reporters after Mass that he was told the issue of clergy sex abuse was taken care of when he became archbishop. | Read the story, watch the video Richard Tsong-Taatarii/Star Tribune via AP

Nienstedt publicly addressed the ongoing clergy sex abuse scandal in the archdiocese head-on Sunday at Our Lady of Grace parish in Edina, telling parishioners and the media that he's sorry he overlooked issues of abuse among parish priests.

He told parishioners and reporters after Mass that when he became archbishop, he was told the issue of clergy sex abuse was taken care of.

"Unfortunately I believed that and so my biggest apology today, and I did this last week at two other parishes, is to say I overlooked this," he said on Sunday. "I should have investigated it more than I did."

Nienstedt, 66, has been archbishop since 2008, after a transition year alongside his predecessor Harry Flynn.

But Nienstedt did not mention the accusation against himself that day, when he celebrated Mass at Our Lady of Grace.

A 1986 archdiocese policy temporarily suspends priests from all "faculties" while the accusation is investigated.

The 2002 Charter for the Protection of Children and Young People approved by the U.S. Conference of Catholic Bishops also prohibits clerics accused of child sexual abuse from celebrating Mass.

In response to Nienstedt's statement that he "overlooked" priests who sexually abused minors in the archdiocese, Richard Sipe, a California-based psychotherapist who is an expert on clergy sexual abuse, emphasized the charter.

Sipe, a Benedictine monk and Catholic priest for 18 years, said he's never heard of case in which a sitting bishop voluntarily steps aside to allow police to investigate child sexual-abuse accusations against him.

The statement from the archdiocese did not identify the person who reported the allegation against Nienstedt. Archdiocese spokesman Jim Accurso declined to comment, referring all questions to the statement.

Auxiliary Bishop Lee Piche speaks to the faithful on the steps of the Minnesota Capitol before the rosary procession May 6, 2012. Piche will cover Archbishop John Nienstedt's public duties while the archbishop steps aside during a police investigation into allegations he touched a boy in 2009. | Auxiliary bishop steps into the breach Alex Kolyer for MPR News

During the investigation, Auxiliary Bishop Lee Piche will assume the archbishop's public duties during the investigation, according to the statement.

However, Sipe said that Nienstedt would remain in charge of the archdiocese since the archbishop did not cede his administrative responsibilities to Piche.

• Related: As Nienstedt steps back, an auxiliary bishop steps into the breach

Nienstedt said he is very concerned about the issue of clergy abuse.

"True, I am a sinner, but my sins do not include any kind of abuse of minors," the archbishop wrote. "I have met victims and I know the lasting damage that such abuse causes."

He also told Catholics that he hopes the investigations "can be thorough but quick."

"I already long to be back in public ministry — to be able to serve as the Lord has called me to serve," the archbishop wrote.

One of Nienstedt's fiercest critics said he hopes the investigation is resolved quickly.

"My initial reaction is 'Oh my goodness, they did the right thing and called the police."

"I feel very sorry for the archbishop. I hope this is just a misunderstanding or some misinterpretation. It's certainly very sad for him," said the Rev. Michael Tegeder, pastor of St. Frances Cabrini church in Minneapolis.

Tegeder said clergy routinely interact with parishioners at Confirmation and First Communion events. He said the interaction could have been in the spirit of a football celebration, in which players congratulate each other.

Tegeder said he's still pushing for Nienstedt to step down, regardless of the police investigation. Tegeder said he's troubled by the way the archbishop has handled the clergy sex abuse crisis, his stance on the recent marriage amendment battle and some of his financial decisions, Tegeder said.

"That's the reason I would still hope he could step down and also just for his own good," he said. "These things can't be very pleasant, and I think it would be good for him to have a fresh start, and it would be good for our archdiocese to have a fresh start and just allow things to move forward here. This is not the way that I would hope that it would come about."

Catholics across the Twin Cities say they're dismayed by the investigation into Nienstedt and the continuous fallout on how the archdiocese has handled the clergy sex abuse scandal. Some say they're pleased the archdiocese reported the allegation against Nienstedt.

"My initial reaction is 'Oh my goodness, they did the right thing and called the police," said Beth-Ann Bloom, parishioner at St. Joan of Arc in Minneapolis. "That's been such an unusual experience in the archdiocese that I'm glad they see what their obligation is."

Barbara Dorris, outreach director for the Survivors Network of those Abused by Priests in St. Louis, said in a statement that "Nienstedt is right to step aside. We hope police and prosecutors investigate this thoroughly and promptly. We also hope that anyone else who might be able to shed light on this allegation will quickly step forward, contacting secular authorities, not church authorities."

But some of Nienstedt's critics are expressing some skepticism about the claim.

Scott Brazil, coordinator of secondary faith formation at Risen Savior parish in Burnsville, Minn., says confirmation photos are typically hurried events during which people are rushed in and out of photo opportunities with the archbishop. Brazil, who said he's no fan of Nienstedt's leadership, says he's not certain any wrongdoing occurred.

"It's not to say that the young person that made the allegations doesn't believe something happened. They very well in their mind might believe it," Brazil said. "I can see how something that was unintentional could have taken place and be taken the wrong way."

Still, the news about Nienstedt is stunning, said Terry McKiernan, founder of the nonprofit website Bishop Accountability.

"Everyone has been wondering whether he can last there in Minneapolis and St. Paul given all the news we've been hearing, but I don't think anyone anticipated the story taking this kind of turn," he said.

On the other hand, it's important to remember that several bishops around the country - not just priests - have been accused of sexual abuse, McKiernan said.