Families, especially children, will likely face more health risks if a new Trump administration plan to hold migrants in detention facilities for longer periods of time goes into effect in 60 days, when flu season will be in full swing, health experts and immigrant rights advocates warn.

Under the new rule, the Department of Homeland Security will be able to indefinitely “hold families together” while their immigration cases are settled in court and provide an “immigration system that is humane,” the agency said Wednesday.

The administration's newly announced rule is a departure from the 1997 agreement known as the Flores Settlement, which requires immigration authorities to release migrant children from their custody within 20 days.

Health professionals and advocates criticized the administration's announcement.

“Already, we have seen the harmful effects of the cruel conditions that resulted from the Trump administration illegally holding children in overcrowded and unsanitary border patrol facilities without access to basic needs and care," said Katie Hamm, vice president for Early Childhood Policy at The Center for American Progress, a nonpartisan research and educational institute. "Removing legal protections for children will remove any protection or standard of care, resulting in potentially irreparable harm to their health and development.”

Concerns over conditions have risen after the deaths of least seven children while in immigration custody under the Trump administration, at a time when a growing number of migrant families are presenting themselves at the border to seek asylum.

At least three of the children died of infectious diseases, such as the flu, over the last year. All three died while in the custody of the U.S. Customs and Border Protection, also known as CBP.

The agency told NBC News in a statement that migrants with the flu “may be diagnosed and treated onsite by CBP medical personnel, or may be referred as appropriate to the local health system for diagnosis and treatment,” adding that CBP currently counts approximately 200 medical personnel engaged along the Southwest border.

However, CBP said it does not routinely administer vaccines against infectious diseases such as the flu, chickenpox and measles, which are normally prevented through vaccinations.

“In general, due to the short-term nature of CBP holding and the complexities of operating vaccination programs, neither CBP nor its medical contractors administer vaccinations to those in our custody,” the agency told NBC News.

Health care advocates took issue with the administration's intent to detain migrant children and families for longer periods of time, warning of the effects on children's health.

“Are they deliberately seeking to create a public health emergency at their detention centers and border communities?” Jim Mangia, president and CEO at St. John’s Well Child and Family Center, one of the nation’s largest providers of health care to undocumented immigrants, said in a statement.

“They’ve already created a dangerous and deadly environment through overcrowding, depreciation of acceptable bedding and unsanitary conditions. Now, by depriving people of a vaccine for a preventable illness, this administration makes it crystal clear that they are willing to put not only immigrant families, but the surrounding communities at deadly risk,” Mangia added.

The CBP holding facilities are often referred to by the people held in them as "hieleras," which translates to icebox or cooler, because of their frigid temperatures. A Human Rights Watch report about these conditions pointed out that children were sleeping under thin Mylar blankets or foil wrappers.

Leah Chavla, an international human rights lawyer and policy adviser at the Women's Refugee Commission, works with families who have raised many concerns over CBP facilities being “inadequate.”

“Families have come with concerns about lack of hygiene, being crammed into holding cells, being served food that has not fully cooked or nutritionally appropriate for kids … being woken up throughout the night," Chavla previously told NBC News.

The American Academy of Pediatrics recommends that migrant families and children should be processed “in a child friendly manner” and “outside current CBP processing."

Regarding vaccinations, CBP said that in certain circumstances, it coordinates with local health authorities and the Centers for Disease Control and Prevention for appropriate support, adding that if a medical professional determines a person requires vaccinations, they would most likely be referred to a local health facility.

Concerns over children's deaths

Carlos Gregorio Hernández Vásquez, 16, died in CBP custody in May after being diagnosed with the flu, an infectious disease. The teenager had spent one week in CBP custody, even though legally he should have not been there for more than three days.

Felipe Gómez Alonzo, 8, also was held in CBP custody for nearly one week before he died Christmas Eve. Medical investigators later determined the boy had been suffering from the flu while he was under the agency’s care.

Days before Felipe’s death, 7-year-old Jakelin Caal Maquin had died in CBP custody, after succumbing to "a rapidly progressive infection" that shut down her vital organs.

In part because of the Flores Settlement, CBP is required to transfer minors into the custody of the Office of Refugee Resettlement (ORR) at the Department of Health and Human Services (HHS) within 72 hours unless there are "exceptional circumstances.

In a statement, ORR told NBC News they do administer vaccinations to unaccompanied migrant children in their custody as well as other kinds of preventive health services.

Even though ORR is more equipped than CBP to house minors for a longer period of time, several children have also died while in ORR care or shortly after being released from immigration custody.

“Children are not like adults. They get sick more quickly and each hour of delay can be associated with serious complications, especially in cases of infectious diseases. Delays can lead to death,” Dr. Julie Linton, co-chair of the immigrant health special interest group at the American Academy of Pediatrics, previously told NBC News.

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