Those initially detained by the government’s Office of Refugee Resettlement are being held until their 18th birthday, then transferred to ICE custody.

WASHINGTON — Isaac, a 17-year-old Guatemalan, crossed the U.S. border nearly eight months ago and was detained as a minor by the U.S. Office of Refugee Resettlement, long before the novel coronavirus existed.

As his 18th birthday approached last month, it appeared he would be released to a Texas shelter where the director promised that the teenager would be “provided counseling and referred for any medical assistance he may require” for high blood pressure, severe anxiety and, if necessary, Covid-19, should the virus reach the shelter.

Instead, on the day he became an adult in the eyes of the U.S. government, agents from Immigration and Customs Enforcement swooped in and shipped him to the Otero County Processing Center in El Paso, where he says he sleeps arm’s distance away from dozens of other immigrants.

“I have no doctor. I have medication but it is one given to me in the previous shelter, when I was a minor,” said Isaac, who asked to be identified only by his middle name for fear of retaliation.

Around 32,000 migrants remain in custody on civil charges as ICE faces growing pressure to address the health concerns posed by the spreading coronavirus, including scores like Isaac who were initially taken into custody as minors, then held long enough to age into the adult detention center. As of Wednesday night, ICE had confirmed 287 cases of the virus among detainees and 35 cases among staff members.

Earlier this year, lawyers representing two migrants argued in a class-action suit that the Department of Homeland Security and ICE had violated a statute that mandates how migrant children should be protected by relying on dubious technology and the discretion of individual local field offices. As a result, instead of minors going to a group home, they are ending up in ICE jails.

The administration’s system of deciding where to place such “age outs” exemplifies the extent of President Trump’s hard-line immigration policies. Those moves include an executive order signed on Wednesday that restricts legal immigration into the United States and obscure procedural maneuvers like age-out detentions that not only limit opportunities to claim refuge in the country but also could expose a vulnerable population to the pandemic. The Education Department this week even prohibited higher education institutions from offering emergency assistance to undocumented students who were brought to the United States as children and are currently protected from deportation.

The coronavirus has re-energized the president’s immigration efforts, even as it brings new scrutiny. A federal judge in California this week ordered ICE to review the cases of detainees at high risk of catching the virus, including those over the age of 55.

But the coronavirus has also amplified concerns over the already contentious — and possibly illegal — practice of moving young migrants like Isaac on their 18th birthday from relatively benign shelters managed by the Department of Health and Human Services’ Office of Refugee Resettlement into the Department of Homeland Security’s ICE detention centers.

While the safest option for the teenagers would be to be released to a sponsor, immigration lawyers say the shelters and group homes would provide more space and care than the detention facilities, where they say the young migrants would be mixed with another contingent population and be exposed to the virus, as well as psychological harm.

“Our clients are terrified of the prospect of being transferred to a secured detention facility with large numbers of people in close, confined settings, which is in direct contravention with C.D.C.’s advice on how to save oneself from this pandemic,” said Anthony Enriquez, the director of the unaccompanied minors program at Catholic Charities, who is representing another teenager in New York who in recent weeks was handcuffed by ICE agents on his 18th birthday and moved to a detention center.

“This is a real recipe for a humanitarian disaster,” Mr. Enriquez said.

Beyond the health risks are legal questions: A federal judge in the District of Columbia will soon rule on whether the Trump administration’s age-out effort violates the law.

By choosing to detain teenagers instead of releasing them to group homes or sponsors, lawyers argue, the administration has violated the Trafficking Victims Protection Reauthorization Act, which requires the government to consider “the least restrictive setting available” to the migrants.

In Houston, ICE agents placed 97 percent of teenagers transferred from the resettlement office’s custody into detention centers as opposed to group homes, according to an analysis of government data from October 2018 to May 2019 submitted during trial. In Miami it was 96 percent and in El Paso 80 percent.

Lawyers for young detainees said the government had proved it did not have to happen that way. An ICE agent from the San Antonio field office, where placement statistics are considerably better, testified during the trial that if the resettlement office had not matched a teenager with a sponsor, he would find a group home that would take the migrant in. ICE agents in San Antonio placed just 2.6 percent of young migrants into detention facilities as opposed to releasing them to group homes or sponsors between October 2018 and May 2019.

“We don’t detain our age-outs,” the ICE officer, Jose Munguia, testified.

April Grant, a spokeswoman for ICE, declined to comment on the details of the continuing litigation. Ms. Grant said that when deciding whether to detain migrants who were aging out, the agency considered whether they were flight risks or dangers to themselves or the community, as well as whether an alternative space was available.

While such transfers occurred in previous administrations, the Trump administration is using a rigged system that ensures immigrants in certain parts of the country will be detained when they turn 18, according to Stephen Patton, one of the lead lawyers in the trial litigated by the National Immigrant Justice Center and Kirkland & Ellis in the District of Columbia. ICE’s computerized “risk classification assessment” system allows agents to enter a migrant’s information, then recommends detention or release.

But according to court documents, the agency tweaked the tool in August 2017 to eliminate the option of release, leaving only the recommendations of “detain” or “supervisor to determine.”

A worksheet requiring ICE agents to document their considerations for alternatives to detention did not include a space to detail the potential shelters available. Agents are left with two options: “detain” or “not detain.”

“There was not a shred of evidence that releasing these kids caused any problems or finding sponsors for them was an undue burden,” Mr. Patton said. “They could comply if they wanted to, and if they do comply almost everyone gets released.”

Another issue with resettling minors has been the Trump administration’s efforts to require sponsors to provide fingerprints to the government. That has discouraged immigrant relatives from coming forward to claim minors in custody, immigration advocates say.

In the 2019 fiscal year, 2,055 migrants were transferred to ICE custody, nearly double the 1,091 in the 2017 fiscal year, according to the Health and Human Services Department. Mark Weber, a department spokesman, said more than 140 young migrants had been handed over to ICE in 2020, but that is a small percentage of the children who cross the border each year and most are eventually matched with sponsors.

Mr. Weber said the department grappled with the most border crossings in more than a decade last year and was still able to place 72,593 children with sponsors. He said “a special effort” was made to release the children before they turn 18.

Ms. Grant, the ICE spokeswoman, declined to say how many of the migrants who turned 18 and were transferred to ICE custody were placed into a group home by the deportation agency.

The agency has also resisted calls for the widespread releases of migrants as the coronavirus approached, though nearly 700 have been released during the pandemic. Matthew T. Albence, the acting director of ICE, told the House Oversight Committee last week that such a move would be a “huge pull factor” and create a “rush at the borders,” according to a statement from the committee. The agency said in a statement that it was continuing to consider releasing immigrants to “alternatives to detention options.”

Those who have aged into the ICE detention centers say the virus has only added to concerns that include threats from fellow detainees, poor treatment by the staff and a lack of medical resources.

Sulma Hernandez Alfaro, who fled to the border to escape abusive relatives in Honduras, said she was confused when ICE agents showed up at the government shelter where she was staying in San Benito, Texas, in 2017. She had already been told by the staff that she would be released to a nearby group home, La Posada Providencia, when she turned 18.

Her lawyers’ pleas to ICE to release her to the group home went unanswered, according to court filings.

She said she was threatened by other detainees and treated poorly by the detention center’s staff. On one occasion, a guard yelled at her when she asked for a tampon. When she asked for a spare change of clothes, she was scolded.

“She just yelled at me and said I should just wash it in the sink because that’s why I have hands,” Ms. Alfaro said.

A court ordered Ms. Alfaro’s release in May 2018, six days before she was granted asylum.

Those are the same protections Jose Hernandez Velasquez hoped to obtain when he crossed the border in 2017.

Mr. Velasquez was erroneously moved from the custody of the Office of Refugee Resettlement as a 17-year-old after he was given a dental exam that mistakenly determined he was an adult, according to his lawyers, who later obtained a birth certificate proving he was a minor. By then he had already spent 10 months in a maximum-security detention center. Such dental assessments are supposed to be used to determine ages only in conjunction with other evidence.

“They told me that I was over the age and I wasn’t a minor even though I pleaded with them that I was. They just took me away,” Mr. Velasquez said in a February telephone interview from the Adelanto detention center in California.

He was placed back into a detention facility when he turned 18. In addition to facing threats from other detainees, he said he developed depression and hypertension while detained.

A federal judge this month ordered Mr. Velasquez to be released after his lawyers said in court filings that he was “vulnerable to serious disease” and that there was danger of the coronavirus spreading “uncontrollably with devastating results” in the detention center.

Mr. Velasquez is now quarantining himself as a precaution. But before he went to self-isolate in Los Angeles, he asked his lawyer to stop by the beach. He had not seen the ocean in nearly three years.

Kitty Bennett contributed research.