As pressure mounted earlier this year to show improvements in New York City’s troubled jails system, its commissioner, Louis A. Molina, made a major change in how the agency responds to violent incidents and staff misconduct.

He took the Department of Correction unit that investigates deaths and serious injuries at the Rikers Island jail complex, which had largely operated independent of the commissioner, and put it directly under his control.

The effect was immediate — but not on the conditions in the jails. The unit and the department resisted sharing information with federal officials overseeing reforms on Rikers, withholding details about at least one disturbing incident that had not been properly documented in the agency’s records.

The commissioner’s taking direct control over the unit that conducts sensitive internal investigations, which has not been previously reported, and the new unit’s lack of cooperation with the monitoring team, were part of a broader move away from transparency that has angered federal authorities. It has brought the city jails system closer to a federal court takeover than perhaps at any point in its more than 120-year history.

Last week, the Manhattan U.S. attorney, Damian Williams, called for an outside authority to take control of the jails, saying that “after eight years of trying every tool in the tool kit we cannot wait any longer for substantial progress to materialize.” And the federal judge who appointed the monitor as part of a civil rights case against the jails, Laura Taylor Swain, has recently signaled a deep frustration with the city’s Correction Department.

For his part, Mr. Molina and his staff members have touted progress, pointing to department statistics that show a decrease in deaths, as well as in slashings and stabbings.

But the creation of the new, tight-lipped investigative group — known as the special investigations unit — and other moves emanating from the commissioner’s office have called into question whether such statements can be trusted, records and interviews show.

While there is nothing inherently wrong with a commissioner changing the structure of the units within the department, former correction officials say, the new unit’s refusal to divulge details of one violent incident has hampered the work of the monitor and other watchdog groups.

The unit that is now being criticized was created on the same day in April that the federal monitor, Steve J. Martin, filed a report with the court praising the department’s willingness to take steps toward reform.

“Real change has occurred,” the monitor wrote in a report filed on April 3. “The practice and cultural changes that are being initiated have real potential to move the department toward reducing the imminent risk of harm faced by people in custody and staff.”

As the department resisted sharing information on violent incidents, the tone of his reports shifted dramatically.

In May, Mr. Martin accused the commissioner and the department of trying to keep secret five serious incidents, including the deaths of two people in custody, and took direct aim at Mr. Molina’s leadership.

Last week, for the first time since he was appointed by the court in 2015, Mr. Martin asked Judge Swain to consider holding the department and Mr. Molina in contempt for disobeying court orders to share information.

The relationship between the commissioner and the monitor began to take a turn in May, when Mr. Martin learned that a 39-year old detainee who had been tackled by correction officers earlier that month had suffered serious injuries and was paralyzed from the neck down.

The correction department’s investigation division reviewed the incident, but some two weeks afterward still had not updated the agency’s records to reflect the hospitalization for critical injuries. Such reports are important for more than just internal record-keeping — they also are circulated to the monitor and a city jails oversight board.

A similar reporting failure occurred on May 14, when a 52-year-old detainee died after plummeting from the top tier of a jail psychiatric unit. The department did not report the incident for 33 hours, records show, and the monitor learned about it only through news reports.

Over the next six days, Mr. Molina and jail officials did not document or delayed reporting three other serious incidents, according to the monitor’s reports. One involved a man who was beaten by other detainees so severely that it ruptured his spleen; afterward, he was left alone, naked, in a cell for hours. Another man died days after suffering a skull fracture — it was not clear how — while in custody; at first, jail officials incorrectly suggested that he had a heart attack, the monitor said. The case is now being examined by the new investigative unit.

A third case involved correction officers who forcibly restrained an 86-year-old man who was subsequently hospitalized. The monitor said in a report that he learned of these incidents, too, not from the department but through external tips.

At one point, the monitor said in his report, he sought a briefing from the new investigative unit about the man who had ruptured his spleen, but the unit never responded. Mr. Molina later told Mr. Martin, “I don’t know what you would expect” from a briefing and noted that “briefings on ongoing investigations are hardly the norm.”

In a June interview with The Times, Mr. Molina said he would never instruct his staff not to speak to the monitor.

“We may have some issue to say, ‘Well, is this really related to the consent judgment?’” Mr. Molina said. “And if we have a difference of opinion, that we can confer with like the law department to get guidance and sometimes that may delay our response to the monitor. I’m not saying delay it a month or weeks, but just because we want to be thoughtful about the answer.”

When he was appointed in 2022 by Mr. Adams, Mr. Molina inherited a correction system on the brink of collapse. He pledged to turn the system around, and assured federal officials that the city could do so without being stripped of control over its jails.

But as detainees continued dying last year, Mr. Molina took steps to limit public reporting of the incidents. In September, he told subordinates to ensure that a dying man was kept “off the department’s count,” The Times reported.

By January, Mr. Molina had made it more difficult for the Board of Correction, a jail oversight panel, to access video and other information from Rikers Island that might point to breakdowns. In May he ended a department practice of informing news outlets when deaths occur.

By the end of 2022, 19 people had died in the city’s jails or at hospitals soon after release. Another seven have died this year, including four this month alone. After the latest death on Sunday, an assistant deputy warden and two officers were suspended for procedural violations related to overseeing detainees, the department and a person with knowledge of the matter said.

In reorganizing the investigative unit in April, Mr. Molina separated it from the department’s Investigations Division, which now only reviews use-of-force cases involving guards.

There were advantages to having all investigative units under the same division, said Sarena Townsend, the department’s former chief of investigations. Under the old model, investigators could work collaboratively, particularly on cases that might touch on multiple fronts, like excessive force cases and deaths in custody, said Ms. Townsend, who became an outspoken critic of the agency after she was fired last year for refusing Mr. Molina’s request to “get rid of” 2,000 discipline cases, she said.

“If you want a good investigative unit, you don’t split it in half,” Ms. Townsend said.

Ms. Townsend said that it was also unusual that the new investigative unit had to answer directly to the commissioner on a day-to-day basis.

“That literally corrupts the entire process,” she said, adding that “if there is no independence of the investigation division then there is no investigation division.”

Before the formation of the new unit, the Investigations Division was run by a longtime associate of Mr. Molina’s, Manuel Hernandez. But Mr. Hernandez resigned in March amid criticism from the monitor that Mr. Hernandez’s investigators were being influenced or prompted to adopt a more lenient approach to internal reviews of excessive force complaints.

Days after the resignation, Mr. Molina reorganized the bulk of the unit to report directly to the commissioner’s office. In addition to death investigations, the newly organized unit handles sex assault cases and runs the department’s canine squad, among other things.

The new special investigations unit is run by Jonathan Levine, who joined the department in December as assistant commissioner after 35 years with the New York Police Department, and who has been described as a loyal ally of the commissioner. Mr. Levine recently suspended a correction captain after the captain complained that the jails were being poorly managed.

Hurubie Meko contributed reporting.