Among the most pressing needs is remaking the department’s disciplinary system, which seems incapable of holding violent guards accountable.

In December, during a meeting of correction officials, Mr. Ponte complained that he had only recently been able to sign off on disciplinary action against a captain who had left the department two years earlier, according to a city official who was briefed on the meeting. Mr. Ponte also expressed concern that the process was badly backlogged because of understaffing and low salaries in the department’s trials and investigations divisions.

One of the cases discussed at the meeting involved Officer Ramel Small. In June, Mr. Small had begun arguing with an inmate named Tamel Brantley, then punched him in the face with a set of keys in his hand, an investigative report said. Mr. Brantley’s eye socket and nose were broken, and he was kept handcuffed on the floor for over an hour without medical attention, the report said. Six months after the episode, Mr. Small still had not been interviewed by department investigators.

With a disciplinary system that is so feeble, there are officers who have been allowed to abuse inmates again and again, another issue highlighted in the United States attorney’s report.

One guard, Bob Villette, who joined the department in 2006, has been involved in at least 88 uses of force, according to department records. He has also been named in seven lawsuits, costing the city $450,000 in settlements for, among other things, cracking the teeth of one inmate and rupturing the eardrum of another.

Mr. Villette, who declined to comment when reached by phone, is a member of the elite emergency services unit, which specializes in subduing disruptive inmates. Including overtime, he has made over $100,000 annually in recent years, city personnel records show.

In December, he got into a struggle with Leon Barnes, an inmate whose arm was in a sling at the time. According to a department report, Mr. Villette wrestled the inmate to the floor, where five other officers “applied control holds” and handcuffed him.