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The New York City Correction Department has been under intense pressure to address systemic brutality and corruption at Rikers, the country’s second-largest jail complex. Credit Richard Perry/The New York Times
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In a major shake-up at the New York City Correction Department, three high-ranking officials, including the top uniformed officer, are stepping down amid mounting criticism over the handling of violence and corruption at Rikers Island.

The chief of department, William Clemons, and two deputies — Joandrea Davis, the bureau chief of administration, and Gregory McLaughlin, the bureau chief of facility operations — are departing, correction officials said. The surprise departures came just five months after all three were appointed to their current posts by Mayor Bill de Blasio’s correction commissioner, Joseph Ponte.

A department spokesman said the changes were the result of “a restructuring” by Mr. Ponte in an effort to halt brutality on the most violent cellblocks.

The department has been under intense pressure from lawmakers and federal and city investigators to address systemic brutality and corruption at Rikers, the country’s second-largest jail complex. The United States attorney’s office for the Southern District of New York, which in August released a damning report detailing abuse of adolescent inmates at Rikers, has threatened to sue the city if changes are not made.

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William Clemons, right, chief of the New York City Correction Department, with Joseph Ponte, the correction commissioner, at a meeting in July. Credit Jake Naughton/The New York Times

The highest-ranking official in the group, Mr. Clemons, is a 29-year veteran of the department. But he has been under scrutiny since an investigation by The New York Times in September uncovered details from an internal Correction Department audit that found he had “abdicated all responsibility” in his duties as warden of a juvenile facility at Rikers in 2011, where hundreds of inmate fights had been omitted from official statistics. The audit recommended that he be demoted.

Instead, he was promoted several times. And The Times found that large sections of the audit, including the recommendation for demotion and the sharpest criticism, were removed from the report by the previous commissioner, Dora B. Schriro.

Mr. Ponte has said he did not see the unedited version of the report before appointing Mr. Clemons chief of department in May. The commissioner promoted him over the objections of the city’s Department of Investigation, The Times found.

In a statement released on Tuesday morning, Mr. Ponte wrote that Mr. Clemons had “proved himself an able leader” and “was a model of stability in a tumultuous time.” Mr. Ponte said he would appoint a new chief by Dec. 1.

Ms. Davis, who joined the department in 1988, is Mr. Clemons’s sister-in-law. She served as warden of three of the 10 jails at Rikers, including the women’s detention center, before moving to administrative positions. Reached by telephone, she declined to comment.

Mr. McLaughlin has been with the department for 27 years and has held several posts. He was warden of the Robert N. Davoren Center, an adolescent jail at Rikers, during a period of extreme violence, and was removed from that command in 2008 shortly after Christopher Robinson, an 18-year-old inmate, was beaten to death by fellow inmates. Mr. McLaughlin could not be reached for comment.

Ms. Davis, Mr. McLaughlin and Mr. Clemons were promoted to their positions shortly after Mr. Ponte’s arrival in April. Ms. Davis will leave her position on Nov. 1, while Mr. Clemons and Mr. McLaughlin are to step down on Dec. 1.

In an interview on Tuesday, Mr. Ponte said that he was now reorganizing the department to improve oversight of the most violent jails at Rikers. This includes getting high-ranking officers out from behind their desks and onto the cellblocks for the majority of their workweek.

He has also designated a civilian, James E. Dzurenda, the former commissioner of Connecticut’s state prisons, to oversee the top ranking chiefs. The change represents a shifting of authority from the traditionally dominant uniformed staff.

The de Blasio administration has also been looking for ways to bring in new leaders, announcing in September that it was seeking to change civil service laws to allow the hiring of high-ranking correction officers from outside the department.

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Joandrea Davis is the bureau chief of administration. Credit Michelle V. Agins/The New York Times

Under the reorganization, Mr. Ponte said he eliminated several top uniformed positions, including those of Ms. Davis and Mr. McLaughlin, prompting them to leave.

“We want to kind of take a look from the ground up with new eyes in these positions,” he said.

Asked whether Mr. Clemons was pressured to step down, Mr. Ponte said it was the chief’s “personal decision.”

Earlier this month, at a City Council hearing about violence at Rikers, Mr. Ponte praised Mr. Clemons for a “long history of doing good work in the agency.”

Lawmakers were not so kind.

Citing The Times’s investigation, the Council speaker, Melissa Mark-Viverito, criticized Mr. Ponte for failing to fire Mr. Clemons, calling the department chief “clearly incompetent.”

In a joint statement released on Tuesday, Ms. Mark-Viverito and Elizabeth Crowley, a council member and the chairwoman of the committee overseeing Rikers, urged Mr. de Blasio and Mr. Ponte to seek out new leadership.

“For too long, the Department of Correction has been rife with the mismanagement and mistreatment of inmates, and the Council’s oversight has only served to further shed light on the deep-seated issues plaguing the D.O.C.,” the statement said.

In the face of the harsh criticism directed at Mr. Clemons, some of his strongest support came from the powerful correction officers’ union and its president, Norman Seabrook. After the Council hearing, Mr. Seabrook’s deputy, Elias Husamudeen, wrote on the union’s website: “I feel like this Council is calling for the head of Chief Clemons.” But on Tuesday, union officials declined to comment on Mr. Clemons’s departure.

Mr. Clemons has largely kept a low profile since the Times report. He did not attend the recent Council hearing, prompting Councilwoman Crowley to say that he “did not have the backbone to appear.”

On Monday, Mr. Clemons arrived at the commissioner’s office at 7 a.m., before the regular staff meeting, Mr. Ponte said.

Mr. Ponte recalled, “He came in and said: ‘I decided to put in my papers; I’m going to retire. I think it’s time.’ ”