Longtime Roman Catholic Bishop Richard Malone, who weathered criticism in two states over his handling of child sexual abuse allegations among the clergy, resigned Wednesday under mounting pressure.

Malone, a Massachusetts native, led Maine’s diocese, the Roman Catholic Diocese of Portland, from 2004 to 2012 before moving to the much larger diocese in Buffalo, New York. For more than a year, he had resisted calls that he should step down, saying last September that a “shepherd does not desert the flock at a difficult time.”

More recently, though, two key members of Malone’s staff have gone public with concerns about his leadership, The Associated Press reported. His former secretary, the Rev. Ryszard Biernat, secretly recorded Malone calling a then-active priest “a sick puppy,” but Malone took no immediate action to remove him. And his executive assistant, Siobhan O’Connor, leaked internal church documents after becoming concerned that Malone had intentionally omitted dozens of names from a publicly released list of priests facing credible allegations of abuse.

Many of those allegations were reported by the Buffalo TV station WKBW and investigative reporter Charlie Specht.

The Vatican announced Malone’s resignation in a brief statement Wednesday, adding that Pope Francis had named the bishop of Albany, New York, Edward Scharfenberger, to oversee the Buffalo diocese temporarily until a permanent replacement is found.

The Vatican did not say why Malone was resigning two years before the mandatory retirement age of 75, although it had conducted a recent investigation into the western New York diocese and Malone’s handling of abuse cases. The Buffalo diocese has been named in more than 220 recent lawsuits by people who claim they were sexually abused by priests.

Malone, in a letter dated Wednesday, acknowledged the “tremendous turmoil” his diocese had endured.

“Some have attributed this to my own shortcomings, but the turmoil also reflects the culmination of systemic failings over many years in the worldwide handling of sexual abuse of minors by members of the clergy,” he wrote. “The crisis our church is facing relates not only to the immoral and criminal acts of those who committed unconscionable offense toward the most vulnerable, but also to the failure to regard these violations as grave offenses that warranted the full weight of civil and ecclesiastical justice.”

Malone also wrote that he had met with many victims and their family members during his time in New York and “felt deeply their anguish,” and said he had worked diligently with others to enact new policies meant to rebuild trust and ensure safety. Ultimately, though, he said the diocese deserved a change.

“I have concluded after much prayer and discernment that the spiritual welfare of the people of the Diocese of Buffalo will be better served by a new bishop who perhaps is better able to bring about the reconciliation, healing and renewal that is so needed,” he wrote.

Malone signed the letter as bishop emeritus of Buffalo.

Prior to being installed as Maine’s bishop in 2004, he spent most of his adult life in Massachusetts, including under Cardinal Bernard Law, the Boston priest who figured heavily in the sex abuse scandal that was reported extensively by the Boston Globe in the early 2000s.

While in Maine, Malone’s tenure was marked by an ambitious consolidation of the state’s parishes beginning in 2005; a prominent but controversial role in the 2009 effort to overturn a same-sex marriage law; and the continued residual effects of the priest sex abuse scandal.

As was the case in Maine, many of the abuse claims in Buffalo date back decades, long before Malone’s arrival in 2012. But critics say there have been more recent missteps by Malone, including his decision to return to ministry a priest who had been suspended by a previous bishop for including “love you” in a Facebook message to an eighth-grade boy. Malone later endorsed the same priest for a job as a cruise ship chaplain, even after he was also accused of making unwanted advances toward young men.

Pressure on him to leave has been intense.

In addition to the damning accounts of former staff members, in September a group of lay Catholics that had been working with Malone to restore trust in the church instead joined in calls for his resignation. A diocesan priest also has been circulating a “no confidence” letter for signatures.

The Vatican recently conducted an inquiry into the Buffalo diocese to get to the bottom of the problems. Bishop Nicholas DiMarzio, who led the inquiry, said he’d finished his work after making three trips to western New York and interviewing about 80 people in and outside the church.

DiMarzio’s report to the Vatican has not been made public.

Among those who have called for Malone’s resignation is the former dean of seminarians at the diocese’s Christ the King Seminary. In a letter outlining his decision to withdraw from his studies to become a priest, Stephen Parisi called the diocese’s handing of clerical sexual abuse cases “disgusting and revolting” and raised questions about the institution’s academic practices and oversight.

Malone in April suspended three priests after several seminarians complained the older men subjected them to disturbing and offensive sexual discussions during a party at a rectory.

Reporting by WKBW also shed light on his handling of allegations during his time in Maine. Internal documents obtained by the TV station detailed summaries of investigations conducted by John S. Brennan, a former police officer who had been director of the Office of Professional Responsibility for the Diocese of Portland under Malone, that were critical of the bishop’s role.

“With respect to the Vatican and Bishop Malone,” he wrote in one report, “this was a complete cover-up of the highest order that cannot possibly be explained or defended and still screams out for justice.”

In refusing previous calls to step down, Malone had said he wanted to be part of the “renewal” of the diocese, which comprises 169 parishes – 32 churches in the city alone – as well as seven colleges and universities, 15 high schools and more than 600,000 Catholics.

The diocese has paid out more than $18 million to more than 100 abuse victims under a compensation program established last year. Since August, it has been named in a wave of new lawsuits under a New York state law that suspended the usual statute of limitations and opened a one-year window for victims to pursue claims regardless of when the abuse happened.

Attorneys general in several states, including New York, have begun civil investigations into how the Catholic church reviewed and potentially covered up abuse.

Reporting from The Associated Press was used in this story

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