When a man was beaten on Rikers Island in December, guards at the New York City jail complex downplayed his injuries, delaying filing a report and then including only minimal information: Fractured eye socket. Swelling of the head. No hospitalization required.

The reality looked much different. Hours after another detainee slammed the man, Jose Matias, 25, to the floor and kicked him in the head, Mr. Matias began having seizures. He was taken to a hospital, where doctors removed a chunk of his skull to ease swelling in his brain. He spent six weeks in a coma and, when he emerged, had to relearn how to walk and talk.

It was at least the second time in four months that the Department of Correction had failed to document a serious injury to a person in custody, records and interviews show. In the other case, in August, a man being held in an intake cell was beaten so badly by another detainee that he was paralyzed from the neck down. No reports were ever filed, and, as far as the jail system’s records were concerned, the assault never happened.

For all of the alarms that have been sounded over rising violence and disorder on Rikers Island, the two cases raise an astonishing prospect: that the levels of brutality experienced by detainees over the past year might have been even worse than was previously known.

The episodes also raise questions about the thoroughness of an incident-reporting process that is supposed to give the public an accurate picture of violence inside the jails and equip policymakers with data on which to base decisions.

It is a system that has broken down in the past. Investigators with the Department of Correction found in 2012 that a warden and his deputy had omitted hundreds of detainee fights from departmental statistics to make their jail seem safer than it was. A review by the Board of Correction, an oversight panel, in 2019 found that the department was frequently underreporting serious injuries sustained by people in custody, and when reports were filed important information was often missing.

And The New York Times reported in January that jailers had failed to document the harm that befell detainees who were forced by a gang leader to participate in a “fight night” while other incarcerated people cheered them on.

But the injuries suffered by the two detainees in August and December — which have not been previously reported — occurred at a time when Rikers Island was already under intense scrutiny for its high rates of violence, and as members of Congress were calling for the Biden administration to step in.

A Department of Correction spokeswoman said both incidents were under investigation. Louis Molina, the jails commissioner, declined to be interviewed. He said in a statement that he had identified deficiencies within the department and intended to “correct the dysfunction” that he inherited from the previous administration, but he did not elaborate.

Appointed in January by Mayor Eric Adams, Mr. Molina is facing the worst crisis to befall the city jail system since the crack epidemic crested in the early 1990s. After the coronavirus pandemic first swept through, thousands of correction officers stopped going to work. Gang members gained control over some housing areas, and other detainees were left to fend for themselves, often going without food or basic health care. Rates of violence rose sharply.

At least 16 people died after being held in the jail system last year — many in preventable ways — and on Sunday Rikers Island recorded its first death in 2022, officials said, after a 38-year-old man, Tarz Youngblood, was found “unresponsive” inside the George R. Vierno Center and doctors were unable to revive him.

“One of my main priorities is to streamline our data analysis and reporting structures, which will allow us to provide accurate and timely information to our stakeholders,” Mr. Molina said in the statement.

Tens of thousands of detainees were hurt last year in the jail system, city records show. More than 1,900 suffered lacerations, concussions or broken bones. Of those, at least 450 were injured so severely that they had to be hospitalized — nearly triple the number in 2020.

No city official can address the problems on Rikers Island without an accurate incident-reporting system, said Bryanne Hamill, a former member of the Board of Correction.

“It paints a very different picture,” Ms. Hamill said, “if the mayor and his staff are not given the proper information to understand the seriousness of what is occurring on Rikers.”

‘His whole life is over’

Khaled Eltahan spent years working blue-collar jobs before drug addiction knocked his life off course, his sister, Fatima Power, said in an interview.

Hooked first on prescription painkillers and then on heroin, he stole batteries, razors, power tools and other items from pharmacies and hardware stores to support his habit, amassing a lengthy arrest record.

Records show he pleaded guilty to a number of charges related to thefts in Queens last summer and was sent to Rikers Island to serve out a 60-day sentence.

When Mr. Eltahan arrived on Aug. 18, the jail complex was in free fall. Staffing problems were causing delays in processing new detainees, leading some men to spend days or weeks packed into intake pens designed to hold people for only 24 hours at a time.

Guards led him into a cell about noon, according to a person with knowledge of his case, who, like others interviewed about Mr. Eltahan and Mr. Matias, spoke on condition of anonymity to describe matters that are actively being investigated.

Mr. Eltahan retreated to a space on the floor, said Anthony Lopez, who was being held in the same cell on a parole violation charge and who, after examining a photo of Mr. Eltahan, said that he was certain he witnessed what happened to him that day. His account was corroborated in large part by details Mr. Eltahan’s sister said he shared with her soon after his release.

Mr. Lopez said Mr. Eltahan lay down, and his pants sagged low enough to partially expose his buttocks. The sight angered a gang member, who ordered him to adjust his clothing and then began kicking him furiously in the stomach, back and head, Mr. Lopez and Ms. Power said.

Soon after, it was clear that something was wrong with Mr. Eltahan. He did not move from a fetal position, Mr. Lopez said, and he spent what seemed like hours begging officers for help. “He said, ‘I can’t feel,’” Mr. Lopez said. “Nobody came to get him.”

About five hours after Mr. Eltahan entered the cell, officers with helmets and batons filed in, according to the person with knowledge of the case. Then medical staff arrived, loaded Mr. Eltahan onto a gurney and took him to the clinic.

At one point, an orderly accused him of faking paralysis and pushed him off the cart, Ms. Power said her brother told her. Mr. Eltahan landed on the floor and struck his head again.

It was not until after midnight that he was taken to a hospital by ambulance, according to the person with knowledge of his case.

At Elmhurst Hospital, doctors discovered that Mr. Eltahan had been paralyzed from the neck down and suffered broken ribs and collapsed lungs, Ms. Power said. He spent three weeks in a coma — during which a state judge granted him time served in a bedside proceeding. A ventilator whirred in the background.

In December, Mr. Eltahan, 41, was transferred to a nursing home in Far Rockaway. He developed sores on his body from being unable to move his limbs. Recently, he caught pneumonia and was hospitalized and placed on a ventilator again, his sister said.

“His whole life is over,” Ms. Power said. “I wouldn’t wish this upon anybody.”

Reporting failures

About three weeks later, a monitor who was appointed by a federal judge to oversee reforms on Rikers Island learned about the beating of Mr. Eltahan — it was not clear how — and asked jail officials for more information, according to the person with knowledge of the case.

Top jail investigators checked the agency’s records but could find no trace of the beating, the person said. The city’s Department of Investigation opened a criminal investigation into the jail system’s handling of the case. Ms. Power said investigators interviewed her brother in September.

The apparent reporting failure occurred despite pledges by Department of Correction officials to do a better job of accounting for serious injuries. After the Board of Correction found major gaps in incident reporting in 2018, the city created a computerized tracking system and provided training for jail workers on how to complete injury reports.

The board review also found that seriously injured detainees had to wait, on average, about two hours before receiving medical care and that many incident reports lacked basic information, such as the times the injuries occurred and the names of people who witnessed them.

Mr. Eltahan’s case was still under investigation when Jose Matias was beaten on Dec. 13. The incident began when Mr. Matias, who had been on Rikers Island about a month, awaiting trial for an alleged shooting in 2019, punched another detainee he was feuding with in his housing unit, according to a person familiar with Mr. Matias’s case.

No jailers were guarding the dormitory floor, and an officer had to exit an enclosed observation station to intervene. When the officer left, the other detainee threw Mr. Matias to the floor and kicked him, the person said. Other detainees broke up the fight.

It was not immediately clear to the officers on duty that Mr. Matias had been seriously injured, and he was taken to and from the infirmary at least twice before a jailer noticed a visible pulsing on his head, said Joseph Russo, the leader of the union that represents assistant deputy wardens and deputy wardens.

Only after Mr. Matias began having seizures was he taken to a hospital for emergency skull surgery, said his mother, Najaris Remigio.

He remained in a coma and on life support until early February, said Ms. Remigio, who added that the incident had altered his life. “I don’t know what to say,” she said of her son’s treatment by the jail system. “It’s like they’re not human beings.”

Department investigators received no reports about the beating and learned about it a day later, through word-of-mouth, the person familiar with the case said. The investigators approached the guards on the housing unit and instructed them to file the required paperwork. The report they submitted incorrectly stated that Mr. Matias had not been hospitalized.

The incident remains under review by the Correction Department, and the Bronx district attorney’s office is examining the actions of the other detainee involved. A civil attorney for Mr. Matias has filed a notice of intent to sue the city.

A failure to properly report beatings is not simply a paperwork error, said Sarena Townsend, the jails’ former chief investigator.

It can compromise criminal and administrative investigations, lead to evidence being tainted or lost and make prosecuting cases more challenging. It can also create a false impression of what conditions are like on Rikers Island.

“When individuals are not held accountable, they act with impunity, and that goes for staff and incarcerated people,” Ms. Townsend said. “Violence is going to increase, and it’s just going to continue this cycle of unsafe conditions.”

Jonah E. Bromwich contributed reporting.