Nielsen said she also planned to visit the border later this week to see "first-hand" how medical screenings were handled.
Her statement came after a second child died this month after being in U.S. custody. Nielsen said that prior to the two deaths, it had been more than a decade since a child in died after being in U.S. custody. Officials said six adults in U.S. custody died in 2018.
"Our system has been pushed to a breaking point by those who seek open borders," Nielsen wrote. "Smugglers, traffickers, and their own parents put these minors at risk by embarking on the dangerous and arduous journey north.
"This crisis is exacerbated by the increase in persons who are entering our custody suffering from severe respiratory illnesses or exhibit some other illness upon apprehension," she said, noting that she also has asked federal health officials to investigate an uptick in illnesses among migrants.
The change in procedures come as border authorities reported that some 24,000 kids have arrived at the border this month alone. Additionally, the area near El Paso, Texas was grappling with a tenfold increase in migration just as flu season gets under way. Migrants are often transported in close quarters to stations designed to house adult males, not large families.
U.S. Customs & Border Protection Commissioner Kevin McAleenan called it a "completely new era" with the apprehension of 24,000 children in December alone -- a number he said was higher than any year prior to 2014. He called it “a humanitarian crisis” and noted that CBP facilities were designed for “single adult males, not families.”
McAleenan and other officials have said they believe "coyotes," or smugglers, are going into poor Guatemalan towns and offering families cheap bus rides north under the promise that the U.S. government would allow them inside the country if they travel with children and claim asylum.
“Our system is inviting [migrants] to take that risk," he said.
The death of the 8-year-old Guatemalan boy minutes before Christmas Day -- identified by Rep. Joaquin Castro as Felipe Gomez Alonzo -- has raised questions about President Donald Trump's handling of the unfolding border crisis and what options U.S. authorities have going forward. As U.S. officials became aware that large groups of migrants were moving northward earlier this year, Trump ordered several thousand troops to the border, where they installed concertina wire and other physical barriers.
Border authorities say what they need now are more detention beds, medical personnel and additional resources to process migrants, which are comprised primarily of parents and children. At the same time, border officials are legally restricted on how long they can detain families, providing few options about where to release the families.
Trump has tweeted throughout the Christmas holiday about his insistence that Congress provide money for a border wall, but did not refer to the boy's death.
"We've been sounding the alarms on this for months," an administration official said Wednesday of the influx of families at the border. The official, who spoke on condition of anonymity, said the administration's position was that it was time for "Congress and the courts" to act.
Local officials in El Paso have accused Immigration and Customs Enforcement of dumping 200 migrants at a time at bus stations and at privately run shelters that say they are out of room.
A 7-year-old girl, Jakelin Caal Maquin, had died earlier this month. Officials said that since her death, additional emergency and medical personnel were placed along remote border checkpoints like the one where she arrived. Officials were in the process of investigating that death when the second child died.
Another looming crisis is the estimated 15,000 children in custody in shelters across the country. These are mostly teens and older children who crossed alone and are waiting to be paired with sponsors. One shelter, Tornillo in Texas, has said it won't accept any more kids and is looking to close its doors by mid January.