The Trump administration, in its continued immigration crackdown, has arrested more than 40 people who came forward to help undocumented migrant children, in a move that is sparking alarm among advocates.

Parents, relatives and friends of children in federal custody can apply to become sponsors and take in minor detainees from government shelters – but authorities are now using their information to pursue and deport such would-be caretakers when they are themselves undocumented immigrants, an Immigrations and Customs Enforcement (Ice) official told Congress this week.

“We’ve arrested 41 individuals thus far,” Matthew Albence, Ice’s acting deputy director, said at a Senate committee hearing. “Our data that we’ve received thus far indicates close to 80% of the individuals that are either sponsors or household members of sponsors are here in the country illegally, and a large chunk of those are criminal aliens. So we will continue to pursue those individuals.”

The arrests came after the federal government in June required all adults living in a home where a migrant child will live to submit their fingerprints to Ice.

The crackdown comes as the number of migrant children in government shelters has shot up to the highest level ever.

It is likely to make relatives who could take in children reluctant to come forward for fear they will be deported, experts say. That means children – mostly adolescents who crossed the border on their own – will stay in government shelters longer, rather than living with family members.

“It’s a terrible thing to do to children,” said Mark Greenberg, a senior fellow at the Migration Policy Institute who oversaw the Office of Refugee Resettlement during the Obama administration.

Ice did not respond to questions about how they determined which potential sponsors would be subject to arrest. An agency official told CNN that 70% of the arrests were for being in the country illegally, as opposed to criminal violations.

Previously, the Department of Health and Human Services’s (HHS) policy has long been not to consider the adult’s immigration status when deciding whether to release a child to a sponsor.

Some Republicans say that should change, and children should only be released to sponsors with legal status.

“If we’re going to take care of children, we’ve got to find a way to be able to take care of children and not put them in the homes of someone who’s not legally present,” the Republican senator James Lankford of Oklahoma said at the hearing.

Robert Perez, acting deputy commissioner at US Customs and Border Protection, said the agency would welcome any change that might reduce “pull factors” that encourage minors to make a journey across the border that is “fraught with danger, fraught with exploitation, fraught with abuse and abandonment at times”.

Currently, HHS continues to allow unauthorized immigrants to legally become sponsors, while the Department of Homeland Security and its Ice agency may arrest and deport them if they apply.

Greenberg said it would be an “enormous disincentive” for parents and others to come forward to claim kids.

“Children will be in shelters for much longer periods of time, which is bad for children and costly for government,” he said, adding that it may also lead to a spike in kids running away from shelters to join their families without informing the government.

Since the new fingerprint policy was announced, the average time children remain in government custody has almost doubled, from 30 days to 58 days, according to Jennifer Podkul, the policy director at Kids in Need of Defense.

“There was already a chilling effect,” she said. “They’re relying on tent cities to hold children, not because there’s an influx of children, but because they’re not getting children out of detention.”

Leah Chavla, a policy adviser at the Women’s Refugee Commission, said many minors are driven to cross the border on their own because of instability and violence in their home countries.

“It’s devastating, because you have situations where parents aren’t going to come forward, and that child languishes in custody,” she said. “It really is cruelty.”