Though there have been serious problems at Rikers for years, the state commission had never before deemed conditions too dangerous for inmate transfers. And it is not clear what prompted the commission to issue the letter when it did. At its two most recent meetings, on March 28 and April 18, the issues raised in the letter were not discussed.

A City Hall spokeswoman said that months before the letter was sent, the Correction Department had submitted plans to address many of the issues raised by the state commission and had started taking steps to resolve them.

“A few minor issues that are already being addressed provide insufficient grounds to revoke a program that has improved the safety of staff and inmates at Rikers and at jails across the state,” said the spokeswoman, Natalie Grybauskas. “We welcome any guidance from the State Commission of Correction on how it believes inmates already in custody at Rikers and around the state should be handled.”

Inmate transfers to jails outside the county of arrest are rare. As of this week, there were 17 transferred inmates at Rikers, mostly from nearby counties like Nassau and Suffolk on Long Island, and Westchester just north of New York City. The letter does not specify what to do with those inmates already in custody at Rikers under the transfer program.

In addition to the 12 jails in New York City, the state commission oversees 63 county jails and 54 state prisons. It evaluates renovation projects and changes in regulations and investigates inmate deaths, among other matters. But it has little enforcement power. In 2015, the commission issued a scathing report about the mistreatment of an inmate at Rikers who was locked in his cell for six days, was denied food and medication and died after he was found naked and covered in feces. The report said the details of the death “shock the conscience.” But corrections officials would not say if anyone was disciplined or fired, and no one was criminally charged.

The commission is but one of a number of agencies responsible for overseeing conditions at New York City jails. In the city, the Board of Correction sets minimum standards that the Correction Department must follow.

The Department of Investigation, which has a special unit for investigating malfeasance at Rikers, has the power to make arrests and refer city employees for prosecution. Since 2014, 38 Correction Department staff members have been arrested as a result of Investigation Department inquiries into brutality by guards, sexual assault and the smuggling of drugs and weapons into Rikers, according to Diane Struzzi, a spokeswoman for the Investigation Department.

There is also a federal monitoring team brought on in 2015 as a result of a class-action settlement over brutality at Rikers. Last month, the team issued a report that said guards were continuing to use brutal force against inmates at an “alarming rate.”