For days after the June prison break by Richard Matt and David Sweat , corrections officers carried out what seemed like a campaign of retribution against dozens of inmates, an investigation by The New York Times found.

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Night had fallen at the Clinton Correctional Facility when the prison guards came for Patrick Alexander. They handcuffed him, took him into a broom closet for questioning, and then, Alexander said in an interview last week, the beatings began.

As the three guards, who wore no name badges, punched him and slammed his head against the wall, he said they shouted questions: “Where are they going? What did you hear? How much are they paying you to keep your mouth shut?”

One of the guards put a plastic bag over his head, Alexander said, and threatened to waterboard him.

Hours earlier, Richard W. Matt and David Sweat had made their daring escape from the unit — called the “honor block” — where they were housed. Now it appeared that Alexander, a convicted murderer who lived in an adjoining cell, was being made to suffer the consequences.

For days after the June prison break, corrections officers carried out what seemed like a campaign of retribution against dozens of Clinton inmates, particularly those on the honor block, an investigation by The New York Times found. In letters reviewed by The Times, as well as prison interviews, inmates described a strikingly similar litany of abuses, including being beaten while handcuffed, choked and slammed against cell bars and walls.

They were also subjected to harsh policies ordered by the state Department of Corrections and Community Supervision: Dozens of inmates, many of whom had won the right to live on the honor block after years of good behavior, were transferred out of Clinton to other prisons. Many were placed in solitary confinement, and stripped of privileges they had accrued over the years — even though no prisoners have yet to be linked to Matt’s and Sweat’s actions.

Indeed, it is prison employees who have been implicated: One has pleaded guilty to aiding the escape; another faces criminal charges; nine officers have been suspended,  and the prison’s leadership has been removed.

More than 60 inmates have filed complaints with Prisoners’ Legal Services, an organization that assists indigent prisoners. And 10 members of an inmate council at Clinton signed a letter last month to state corrections officials making similar allegations.

“We have been daily getting complaints along these lines from around the state,” said Michael Cassidy, a lawyer for Prisoners’ Legal Services.

The Department of Corrections is apparently looking into the complaints. Several inmates interviewed by The Times said  members of the department’s Office of Special Investigations had visited them.

The Times sent questions to the department on Monday morning seeking comment but has not received a response.

The accounts suggest that as corrections officers frantically pressed for information that could lead to the capture of the two prisoners — and perhaps exonerate themselves for the security lapses that contributed to the breakout — they resorted to brutal tactics that most likely violated department regulations.

Victor Aponte, who worked in the prison tailor shop where Matt also had a job, said a guard with an American flag tattoo, known around the prison as “Captain America,” tied a plastic bag around Aponte’s neck in an interrogation and tightened it until he passed out. Reggie Edwards, who supervised the tailor shop, said that corrections officials put him in solitary confinement for three weeks and threw out most of his belongings, including his family photographs and his wedding ring.

After a three-week manhunt, a federal agent shot and killed Matt. Two days later, a state police officer shot Sweat, and he was captured.

Alexander got the news at Shawangunk Correctional Facility in Ulster County, where he had been transferred. He said he earned his place on the Clinton honor block because he had not been written up for any serious infractions since entering the prison system in 2004. He occupied the cell next to Matt, who was in prison for murdering his boss and then cutting up the body. (Long before he cut his way out of prison, Matt was known around Clinton by the nickname Hacksaw.)

For Alexander, his cell’s location apparently made him a target for investigators.

The night of the escape, Alexander said, he worked late at the tailor shop, and when he returned to his cell at about 9:45 p.m., Matt gave him bowls of salad and fried chicken that had been purchased at the commissary. “He told me, ‘Don’t worry about it, I’ll get the bowls from you in the morning,’” Alexander recalled.

He said he was awakened at about 5:15 a.m. for the morning count. “The officer comes banging on the bars. He goes to Matt’s cell and bangs on the bars and then he leaves and he bangs on Dave’s bars.” When there was no response, a sergeant and several guards frantically rushed up and down the cellblock shouting to one another that two inmates were gone, he said.

“The sergeant comes over to me, ‘You hear something? You had to hear something,’” Alexander recalled.

It would be several hours before the first details of the escape were made public. Around 11 a.m., New York Gov. Andrew M. Cuomo toured the honor block and inspected the holes that the inmates had cut in the backs of their cells with hacksaw blades.

The governor then stopped to question Alexander.

“Must have kept you awake with all that cutting, huh?” Cuomo asked, according to video of the exchange. Then, Alexander said, the governor “gave me his best tough guy stare and walked off.”

Later, the governor said he would be “shocked” if any corrections officers were involved.

Twice during the day of the escape, Alexander said that he was questioned by investigators from the State Police and Corrections Department inspector general’s office.

Then, at about 8 p.m., he was handcuffed and taken to a broom closet where, he said, three corrections officers whom he had never seen before interrogated him. An officer wearing a jacket with the initials CIU — Crisis Intervention Unit — sat down and asked him, “Do you know the difference between this interview and those other interviews?” Alexander recalled.

This time, the officer warned, there were only uniformed guards in the room, Alexander said.

“The officer jumps up and grabs me by my throat, lifts me out of the chair, slams my head into the pipe along the wall,” he said. “Then he starts punching me in the face. The other two get up and start hitting me also in the ribs and stomach.”

With each punch, Alexander said, the officers shouted another question.

“The whole time he’s holding me up by my throat,” he added.

When Alexander repeatedly insisted that he had no information, one officer pointed to a plastic bag hanging on some pipes, asked if he knew what it was for and said, “You know what waterboarding is?” Alexander recalled.

The officer then put the bag over his head and started beating him again, Alexander said.

He said the interrogation lasted about 20 minutes, and he was then taken, bleeding, back to his cell.

Later, Alexander said, the same officer “began quietly taunting and threatening me, telling me, ‘Don’t worry, Fat Boy, we’ll be seeing you really soon.’”

In a letter to Prisoners’ Legal Services, Aponte, who also worked in the tailor shop, described going through a similar interrogation two days later.

One officer stood in front of a window blocking the view into the room, he wrote, while another guard in a CIU windbreaker tied a garbage bag around his neck, “using the plastic bag as a hanging noose.”

“I don’t know how long he hung me up like that because I passed out,” Aponte wrote.

Aponte, along with several other inmates, said they were initially denied medical care. Days later, when he was finally taken to the prison clinic, officers warned him not to tell the medical staff how he got his injuries, he wrote in a letter.

“The sergeant tells me that I’ve been in prison for long time and I should know better, that if I didn’t tell the nurse that was going to examine me that nothing has happened that they were going to kill me for real this time,” he wrote.

Paul Davila, another resident of the honor block, wrote in his complaint that after he was beaten during an interrogation, he was pressured to “sign a report stating, ‘I was not assaulted.’”

“Left with no other choice,” he wrote, “I signed.”

In the two weeks after the escape, inmates from Clinton’s honor block were dispersed, many of them sent to solitary confinement at other prisons. Some said they were beaten during their transfers by officers from the department’s Correctional Emergency Response Team, known as CERT.

“The CERT team rushed into my cell, threw me down on the bed, twisted my wrist and yelled at me not to resist,” an inmate, Manuel Nunez, wrote in a letter, adding that later they “assaulted me while I was cuffed, chained and shackled.”

He said when he and other inmates were lined up to board a corrections bus, officers passed by, punching them.

During an interview last week at Sing Sing Correctional Facility in Ossining, New York, Nunez showed reporters purple scars around his right ankle that he said were the result of CERT officers’ intentionally shackling him too tightly.

Some of the former honor block residents have lost privileges that had taken years to earn at Clinton. Edwards, who had supervised 50 inmates at the prison tailor shop, had been able to earn as much as $45 a week. Since being moved to Sing Sing, he has been working as a porter making $3 a week.

“They took everything from me,” he said. “They did everything they could to blame the ones who stayed.”

Alexander said that days after being beaten up, he was moved, first to the Upstate Correctional Facility and then to Shawangunk Correctional Facility. In the process, he said that he lost his TV, his diaries, family photos and a decade’s worth of letters from his mother and aunt that he had laminated with packing tape for safekeeping.

Despite all this, Alexander and many others interviewed said they did not resent the two escapees.

Sweat was serving life in prison with no possibility of parole for shooting a sheriff’s deputy in the back 20 times and then running him over. Faced with that kind of time, some said, they may well have considered escape.

“I can’t say what I’d do; I didn’t have the time Sweat has,” said Alexander, who has spent 11 years in prison and will be eligible for parole in 2023. “So no, I don’t resent them. Maybe I should, but I don’t.”

Inmates insisted that the freedoms awarded on the honor block were not what led to the escape. Investigators have found that it was a corrections officer and civilian supervisor who smuggled in the tools that aided Matt and Sweat. And because of security lapses, officials say, the two inmates were able to spend night after night readying an escape route, cutting through the backs of their cells, a brick wall and a steel steam pipe.

Investigators and inmates say that instead of making hourly rounds of the cellblock each night, as they were supposed to do, most guards slept through much of their shift.

“Laziness caused that incident, not privileges,” Davila said.

Inmates joked that the only ones walking the cellblocks on the overnight shift were the cockroaches.