In more than 60 complaints since the escape, inmates from the Clinton Correctional Facility have claimed they were physically abused, placed in solitary confinement and stripped of privileges, according to the Prisoners' Legal Services of New York, an organization that helps prisoners.
The New York State Department of Correctional Services said the complaints are being investigated by its office of special investigations and have been referred to the state's inspector general.
"Any findings of misconduct or abuse against inmates will be punished to the full extent of the law," corrections officials said in a statement to CNN.
The union that represents state corrections officers decried reports of the inmates' complaints as "one-sided," noting that the law enforcement community has been cooperating with a state investigation into the escape and awaiting the results before speaking out.
"We took this approach because it was a responsible course of action and chose not to counter the wide number of inaccurate facts and misinformation being reported by various new agencies through less than reliable sources," said James Miller, a spokesman for the New York State Correctional Officers & Police Benevolent Association.
"Our course will continue to stay the same regardless of 'allegations' made by a handful of violent convicted felons."
Michael Cassidy, an attorney for the Prisoners' Legal Services, said the organization received more than 60 complaints from inmates after the escape, including allegations that inmates were physically abused, that their cells were searched, that their property was damaged or destroyed and that they were confined -- some for weeks -- without proper procedures followed.
"The quantity and similarity of the complaints is troubling," Cassidy said, adding that inmates' constitutional rights against cruel and unusual punishment may have been violated. Dozens of inmates, he said, were transferred from the prison without due process. Prisoners told the organization they were rounded up in the middle of the night, shackled and transferred -- at times denied clothes or showers for weeks.
And the complaints haven't stopped, he said, with prisoners continuing to allege that privileges are being denied to them and that they are receiving threats from officers at the prison.
"Things are very tense there right now," he said.
Report: Guard threatened waterboarding
After Richard Matt and David Sweat
broke out of the Clinton Correctional Facility in upstate New York in June, investigators were looking for answers -- fast.
Manuel Nuñez, who had been on the honor block with Matt and Sweat, said less than two weeks after the escape, he was transferred out of the prison with no explanation. Guards from the prison's emergency response team, he said, rushed into his cell, threw him on his bed, twisted his wrist and yelled at him not to resist.
As he and other inmates lined up for their transfer out of Clinton, Nuñez said, an officer walked by and punched them, shouting, "If you look at me, I'll beat you up."
On June 16, Nuñez said, he was transferred to a different prison and shackles were tightened on his right ankle and hand. He has a purple scar and bruises on his right ankle that he said are a result of officers gradually making the shackles too tight.
Nuñez said he was kept in isolation for more than two weeks. The only time his door was open, he said, was when investigators came to question him about the escape.
He wasn't the only prisoner being questioned.
In an interview with The New York Times, inmate Patrick Alexander said a guard placed a plastic bag over his head during an interrogation, shouting a series of questions: "Where are they going? What did you hear? How much are they paying you to keep your mouth shut?"
CNN has not been able to independently confirm the details in complaints reportedly filed by Alexander and dozens of other prisoners.
At one point, Alexander alleged to the Times, an officer grabbed him by his throat, lifted him out of a chair and slammed his head into a pipe. Two other officers punched him as they shouted questions, Alexander told the newspaper.
"When Mr. 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?' Mr. Alexander recalled," the Times reported. "The officer then put the bag over his head and started beating him again, Mr. Alexander said."
Alexander told the Times he was bleeding as he was taken back to his cell.
Manhunt lasted for weeks
Matt died after officers shot and killed him
during the manhunt. Sweat made it within two miles of the Canadian border before a New York State Police sergeant tracked him down and shot him
. He has been released from the hospital and is in solitary confinement at another prison.
Meanwhile, Clinton Correctional Facility and its workers have been under increased scrutiny.
Three members of Clinton Correctional Facility's executive team, along with nine security staff employees, have been placed on paid administrative leave as part of the review of the escape, according to the New York State Department of Corrections and Community Supervision.
The FBI is investigating possible broader corruption at the prison, law enforcement officials briefed on the case told CNN. Agents are looking into whether drug trafficking or other criminal behavior among employees and inmates took place, officials said.
Some employees who have been questioned told investigators there was heroin use among prisoners and an alleged drug trade involving employees, the officials said.
The correction officers' union said Tuesday that it's awaiting results of the state's investigation.
"Once the investigation is complete, and we have a chance to review the findings, we will have the opportunity to give our viewpoints," Miller said. "That is the most responsible action to take, and we hope the public will do the same."