ROME — The Vatican on Wednesday announced the resignation of Bishop Richard J. Malone, who stoked fury in his Buffalo Diocese over the alleged mishandling of sexual abuse claims and whose tenure became emblematic of the Catholic Church’s struggle to overcome its central crisis.

Under Malone’s watch, Buffalo had become perhaps the U.S. church’s most scandal-tainted diocese. It faces an FBI probe and more than 200 lawsuits. Malone pledged to institute reforms, but he was instead battered by accusations of engaging in a coverup and by embarrassing leaks. One whistleblower said she found a 300-page dossier on accused priests hidden in a supply closet near a vacuum cleaner.

In a short statement, the Vatican said Malone would be replaced on a temporary basis by Albany’s bishop, Edward B. Scharfenberger.

Malone, 73, is departing two years before the mandatory age at which bishops must offer their retirements to Pope Francis — although many prelates stay on the job beyond the 75-year mark. The Vatican did not explain the reasons for Malone’s resignation. Malone said in a three-page statement released Wednesday that he had asked for and received permission from the pope to “retire early.”

“I have acknowledged on many occasions the mistakes I have made in not addressing more swiftly personnel issues that, in my view, required time to sort out complex details pertaining to behavior between adults,” Malone wrote in the statement. “In extensive listening sessions across our Diocese, I have heard your dismay and rightful concerns.”

Malone’s case offers mixed signals about how the Vatican is dealing with bishops accused of negligence or engaging in a coverup and whether changes drawn up by Francis will help the institution police its upper ranks.

The Vatican did not use a system put in place by the pontiff this year that would have allowed the region’s top bishop — in this case, Cardinal Timothy Dolan of New York — to open an investigation. Instead, in something of an ad hoc measure, the Vatican dispatched a different prelate, Bishop Nicholas DiMarzio, on a “nonjudicial” fact-finding mission to Buffalo.

The Associated Press reported last month that DiMarzio is facing accusations of sexually abusing a child. DiMarzio denies the allegations.

For more than a year, Malone had resisted calls to step down. But the pressure ratcheted up as the revelations seemed to build. In September, a Buffalo television station broadcast audio, secretly recorded by the bishop’s priest-secretary, in which Malone worried about what might happen if the sexual harassment accusations that a seminarian had leveled against a priest became public.

“This could be the end for me as bishop,” Malone said in the leaked recording.

But the situation was even more convoluted. The seminarian, Matthew Bojanowski, accused Malone of failing to act against the parish priest. Meanwhile, news outlets obtained a letter from the bishop’s priest-secretary to Bojanowski that suggested the two had a romantic relationship.

In September, Malone held a news conference at which he awkwardly tried to make sense of the “complex situation” and faced sharp questions about his judgment.

The local congressman called on Malone to resign. So, too, did a council of prominent Catholics. A petition calling for Malone’s departure gathered more than 12,000 signatures, accusing him of deceit and for being a “silent accomplice” to the crimes of priests. A Buffalo News poll in September said that nearly 86 percent of area Catholics wanted him to resign. Picketers had followed the bishop to recent events, and the newspaper reported that the diocese had ceased publishing the bishop’s event calendar.

“Bishop Malone did this to himself by ignoring the problems that existed in Buffalo,” Bojanowski said by email. “He lied to the people, wanting them to think that there was transparency, when all there was were coverups upon coverups.”

“There are many priests in Buffalo that need to be laicized,” Bojanowski continued. “Bishop Malone leaving is just a start, but far from over. Buffalo is in desperate need of a strong leader who will stand up to the many bully priests that don’t want to serve their community, but rather just serve themselves.”

Malone said Wednesday that during his tenure, “there has not been a single priest of this Diocese ordained in the past 30 years who has had an allegation of child sex abuse substantiated.”

Malone has been bishop of Buffalo since 2012. Last month, he traveled with other New York state bishops to the Vatican and met with Francis. After returning, Malone issued a statement that gave no indication he planned to step down.

“In a few words spoken privately to me, it was clear that the pope understands the difficulties and distress we here in Buffalo, and I personally, have been experiencing,” Malone said at the time. “He was very understanding and kind.”

The problems for Malone escalated early in 2018 when an initial accuser alleged molestation as a teenager by a priest. A wellspring of abuse complaints followed, and in March 2018, Malone released a list of 42 priests who had been credibly accused of sexual abuse, mostly from earlier decades. But it was anything but full transparency: Malone’s former administrative assistant had seen an earlier draft of the list. It contained more than 100 names.

Going public on CBS News’s “60 Minutes” last year, the former administrative assistant, Siobhan O’Connor, accused Malone of wiping some of the most problematic names from the public record. One of the missing names was that of a priest who had been accused of inappropriately touching two boys. According to the “60 Minutes” report, Malone endorsed that priest for a job as a cruise ship chaplain.

In a statement, Terry McKiernan, co-director of Bishop-Accountability.org, said Buffalo was a “microcosm” of the U.S. abuse crisis, with accountability coming from survivors, whistleblowers and journalists — not the Vatican. He criticized the Holy See for offering no explanation or contrition alongside the statement of Malone’s resignation.

“Rome has allowed and enabled the slow-motion train wreck of a great American diocese,” McKiernan said.

Michelle Boorstein in Washington contributed to this report.