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New York City’s jails are experiencing a spike in coronavirus cases as the Omicron variant spreads, gravely threatening detainees at the end of a year that has already seen 16 people die after being held in custody.

According to a letter sent by the outgoing Correction Department commissioner, Vincent Schiraldi, the coronavirus positivity rate has jumped drastically in the last several days among incarcerated people, only 38 percent of whom are fully vaccinated. Among city residents, 71 percent are fully vaccinated.

Mr. Schiraldi’s letter, sent on Tuesday to city district attorneys, public defenders and judges, said that the seven-day test positivity rate among incarcerated people had jumped to over 17 percent. Citywide, the seven-day average positivity rate was 11.2 percent as of Monday.

“The risks to the human beings in our custody are at a crisis level,” Mr. Schiraldi wrote, adding that the jail population faced “an equal or greater level of risk from Covid now as it did at the start of the pandemic.”

The department on Tuesday announced that it would suspend in-person visits with detainees as well as programs and services, including religious services, in response to the rise in cases.

A coalition of public defender organizations released a statement calling for the release of those behind bars and urging elected officials, district attorneys and judges to do all they can to stop new jail admissions.

“Without vaccinations, in a congregate setting, with people who often have health problems and are vulnerable for a whole host of reasons, we’re worried about more deaths,” said Tina Luongo, the attorney in charge of the Legal Aid Society’s criminal defense practice, calling for “immediate steps to get as many people off of Rikers as possible.”

Speaking to reporters on Wednesday, Mayor Bill de Blasio stressed that the city was experiencing an intense surge in cases spurred by the Omicron variant, but with far fewer hospitalizations than in previous waves. He added that 85 percent of uniformed staff in the system were vaccinated, after the imposition of a mandate that took effect Dec. 1.

Dr. Mitchell Katz, the chief executive of New York City Health and Hospitals, said that new units had been opened to isolate detainees with the virus from the general population. None of the detainees who recently tested positive required hospitalization, he said.

Spokespeople for the Manhattan, Brooklyn and Queens district attorneys’ offices said that their offices were reviewing cases in which bail had been set or people had been detained, and were working toward the release of those who could be safely freed. The Bronx and Staten Island district attorneys’ offices did not immediately respond to requests for comment.

A spokeswoman for Gov. Kathy Hochul said that the governor had previously taken action to address concerns in jails, and that her administration was “committed to continuing to work with elected partners and advocates on solutions to improve justice and safety.”

Benny Boscio, the president of a union that represents correction officers, blamed Mr. Schiraldi for the surge in cases in the jails, saying that the department had been negligent when it came to ensuring that visitors did not have the virus.

“By allowing visitors to come into our jails without having to show proof of vaccination and without mandating the inmates be vaccinated, Commissioner Schiraldi has once again put thousands of lives in jeopardy,” Mr. Boscio’s statement said.

In the spring of 2020, Mayor de Blasio, along with public defenders and other local officials, helped champion an effort to release vulnerable populations from city jails. That led to hundreds of people being released and the total population of the jails dropping to fewer than 4,000, a low not seen for decades.

But the population rose steadily beginning in the summer of 2020. There are currently about 5,400 people being held in New York City’s jails, most of them at the troubled Rikers Island complex.

The pandemic and a severe staffing shortage have crippled the system on Rikers, leaving detainees in control of parts of the facilities at times. The 16 deaths represent the deadliest year for the jail system since 2013. Several of the deaths were ruled suicides. A federal monitor appointed to oversee reforms recently wrote that the Department of Correction was “trapped in a state of disrepair.”

Jeffery C. Mays contributed reporting.