This story was published in partnership with the Center for Public Integrity.

Newly obtained government documents show how the Trump administration’s now-blocked policy to separate all migrant children from parents led social workers to frantically begin tracking thousands of children seized at the southern border and compile reports on cases of trauma.

In June 2018, months after the Trump administration began its so-called “zero tolerance” policy to deter migrants trying to enter the United States, an employee working for the U.S. Office of Refugee Resettlement described a 5-year-old’s despair at a shelter. “Minor was separated at the border from his biological mother. Minor was tearful when he arrived and would not speak or engage in conversation with anyone,” the caregiver wrote in a report. This document and others shed light on a social experiment that was both cruel and chaotic.

Reports of traumatized children were forwarded to the Department of Homeland Security’s Office for Civil Rights and Civil Liberties, which is charged with ensuring that national security policies respect constitutional rights. A Center for Public Integrity and NPR investigation earlier this year found that the office failed to assist children whose suffering was documented in hundreds of similar complaints the office received last year.

The most recent internal documents Public Integrity reviewed add to scathing criticism from the Homeland Security inspector general’s office, which reported on Nov. 25 that it couldn’t verify how many children were separated by the zero tolerance policy, which began gradually in late 2017 and ended in June 2018. Tracking was flawed because U.S. Customs and Border Protection officers didn’t accurately record possible family relationships between adults and 1,233 children detained between October 2017 and mid-February 2019, the inspector general concluded.

Trump’s zero tolerance policy required CBP to separate children so that migrant adults, many of them seeking asylum, could be immediately held in immigration detention and prosecuted for illegal entry.

Earlier this year, former Office of Refugee Resettlement Deputy Director Jonathan White told Congress that he’d heard in early 2017 a broad separation policy could be in the works, and that he and his colleagues told Homeland Security officials they were concerned “not only about what that would mean for children, but also what it would mean for the capacity of the program.”

Internal records, however, show that such concerns date back further.

Warnings weeks before Trump

Among the documents Public Integrity obtained is a September 2016 email from a child refugee specialist signaling discomfort with Customs and Border Protection’s Office of Field Operations splitting up migrant families prior to zero tolerance.

“The best thing that could happen is for the OFO to stop the practice of family separation,” a child refugee field specialist added to the top of an email containing instructions for reunifying families that he sent to colleagues on Sept. 20, 2016.

Just 10 days after the specialist sent the email, a Homeland Security advisory committee issued a damning report on the damage children suffer when abruptly separated from parents. Separations were comparatively uncommon at the time, but they’d grown frequent enough to trigger a review, conducted by representatives of the American Academy of Pediatrics and civil rights groups.

“Separation can be acutely frightening for children and can leave children in ad hoc care situations that compromise their safety and well-being,” the advisory committee warned. “It can also be traumatizing and extremely stressful for the parent.”

The committee urged Homeland Security to separate parents and children as little as possible and instead place families in supervised release programs while their asylum or other immigration claims moved through the courts.

Before Trump began zero tolerance in 2018, Customs and Border Protection had — and still has — the authority to separate parents and children under limited circumstances.

But because zero tolerance required parents to be immediately detained, CBP was essentially forced to seize thousands of children, including infants and toddlers. Most families were arriving from Central America, a region the State Department has said is ravaged by predatory gangs and homicide rates that are among the highest in the world.

The 2016 message from the field specialist is part of a collection of Health and Human Services emails and other internal documents shared with Public Integrity. Most were written in 2018 by officials at the agency’s Office of Refugee Resettlement, part of the Department of Health and Human Services. The office is responsible for caring for unaccompanied migrant children, or children CBP officers separate from parents at the border. The internal documents show Health and Human Services staff members were unprepared for the unprecedented number of suffering young children transferred to their custody.

The materials were obtained through a Freedom of Information Act request submitted to Health and Human Services by the American Immigration Council, the National Immigrant Justice Center, Kids in Need of Defense, the Women’s Refugee Commission, and the Florence Immigrant and Refugee Rights Project. All have experience providing legal services for migrant children.

Child on floor crying

Most of the internal government emails reviewed by Public Integrity were written during the height of zero tolerance, which ended in late June 2018 after a court order and public outcry. Other documents show Refugee Resettlement staff or contractors’ observations, which then were forwarded to Homeland Security, about distraught children placed in shelters.

A 10-year-old held in a shelter for two months was found on the floor, crying and holding his hand. “My hand hurts because I got mad about my case and I hit the wall,” the boy reportedly said in July 2018. A 12-year-old boy reported “suicidal ideations” after separation from an aunt and a cousin in June 2018, according to a document. In a July 2018 report about a 9-year-old, a case worker wrote the girl “reported that her uncle was murdered by a local gang.”

After a federal judge ordered Homeland Security, Health and Human Services, and Refugee Resettlement on June 26, 2018, to reunite families, emails and other documents show refugee office staff and contractors were pressed into service.

“All resources available to comply with court order,” reads a summary of what’s labeled as a meeting with Health and Human Services Secretary Alex Azar. “We must do everything to identify parents, contact them, and make strides to reunify them or [allow children] to go to another sponsor if the parents want.”

Given the poor quality of records, Health and Human Services officials rushed to use DNA testing to match parents and children.

“DNA kits,” a message to staff advised, “will be sent to programs with separated children 0-4 on week of July 2nd and DNA kits will be sent to programs with separated children 5 and up on week of July 9th.”

DNA collection is controversial. News reports in July featured mothers and a director at a migrant mothers’ shelter claiming they were told parents would have to pay for DNA testing. Health and Human Services denied it was charging fees for the testing and said it was covering costs for collections.

Documents also show that social workers anxiously sought supervisors’ guidance on how to respond to Central American U.S.-based consular officials, who were asking for information about migrant children scattered nationwide.

Robert Carey, a Refugee Resettlement director in the Obama administration, told Public Integrity that most of the office’s staff are social workers who were put in an “ethical” dilemma with the zero tolerance policy.

“Not only was it inhumane,” he said, “it was extraordinarily poorly managed.”

When he was in charge, Carey said, the average minor in Refugee Resettlement custody was about 15 years old. A “large part” of what the office would do, he said, was vet sponsors, often relatives, so children could be released from group shelters or foster homes.

Trump’s zero tolerance has ended, but CBP continues to have the authority to separate children from adults who are not legal guardians, including aunts, uncles and grandparents. It also has the authority to separate children based on a parent’s prior immigration violations, if CBP wants to refer that parent for prosecution. Officers have also separated children due to parents’ criminal histories or suspected ties to gangs — decisions that at times have been based on false allegations.

James De La Cruz, the Health and Human Services employee who wrote in 2016 that ending family separations would be “the best thing that could happen,” is still at the agency.

His email included instructions for reunifying families and a contact sheet for Homeland Security staff assigned to supervise “alternatives to detention” programs. These programs — no longer favored by the Trump administration — monitored migrant families that had been released from custody to ensure they would attend court proceedings.

Contacted by Public Integrity, De La Cruz declined to elaborate on his 2016 email or on problems Health and Human Services faced with the surge in family separations last year. The agency’s media representatives also declined to comment but sent a written statement emphasizing that “HHS is a child welfare agency, not a law enforcement agency. We play no role in the apprehension or initial detention of unaccompanied alien children.”

Under Trump, however, Health and Human Services was forced into a central role in the administration’s zero tolerance policy because separating children from migrant parents was a key feature.

Separating kids to block asylum seekers

Despite evidence from the State Department and others supporting many migrants’ stories of escaping violent crime in their home countries, Trump accused migrants of gaming the asylum system, and he sought ways to block their entry. After he took office in 2017, his advisers suggested options that would require prosecuting every border crosser. Separating thousands of their children “would be reported by the media and it would have substantial deterrent effect,” previously released documents shared by NBC show.

As a pilot program began in 2017, people who swam or walked over the border or who approached CBP officers at border gates were taken into custody to be prosecuted for illegal entry — a misdemeanor the first time — and their children were taken from them.

Preparing for a blanket separation policy, then-Attorney General Jeff Sessions spoke out in defense of family separations in May 2018. “If you don’t like that, then don’t smuggle children over our border,” he said.

That same month, however, Refugee Resettlement officials were already sending out “high importance” emails related to the developing search for separated families.

Like Homeland Security, the office had come under pressure because of a lawsuit filed by the American Civil Liberties Union three months earlier. The lawsuit accused Homeland Security, Health and Human Services, and Refugee Resettlement of violating due process and Homeland Security’s own directives for granting detainees’ release.

The initial plaintiff was an African mother who was cleared at the U.S.-Mexico border to apply for asylum but was put into detention. She said she heard her daughter, 7, screaming as the child was taken away to be sent to Refugee Resettlement custody.

Eventually, the lawsuit became a class-action effort to free and unite separated families.

On May 16, 2018, a Refugee Resettlement email exhorted staff to find the parents of children in their custody — one day after then-Homeland Security Secretary Kirstjen Nielsen testified in Congress that “we do not have a policy to separate children from their parents.”

“It is very important to locate the separated parent for all UAC [unaccompanied alien children] in your program,” a Refugee Resettlement supervisor wrote. “For parents in ICE [Immigration and Customs Enforcement] custody, you should be able to locate them and have a phone call with that parent as soon as possible.”

That assumption proved far too optimistic.

CBP, it turned out, was sending children to Refugee Resettlement with little information about parents. Infants and sobbing toddlers were too young to know parents’ names, as Public Integrity previously reported, much less the “alien number” that ICE assigns adult detainees and enters into a detention database.

“The system totally broke down,” said Jennifer Podkul, an attorney with Kids in Need of Defense, which coordinates legal representation for migrant minors. Even lawyers who know the names of clients have a hard time using the ICE detainee tracking system because of misspelled names and other erroneous information, she said.

One internal email warned social workers “to NOT engage directly” with the ACLU, as one caregiver program did, and instead follow “the chain of command” to prepare for a child’s release.

‘Initiate contact with parents!’

On June 26, 2018, the federal judge in San Diego presiding over the ACLU’s lawsuit admonished U.S. officials for tracking migrant children with less diligence than they track belongings the government seizes from people and keeps in storage. He placed a preliminary block on further separations, ordered officials to arrange phone calls between parents and children, and reunite them on deadlines by age group the following month.

Emails show Refugee Resettlement staff discussed how to arrange and pay for collect calls from detained parents, and how parents were incommunicado while held in federal marshals’ custody, as many were at times.

On June 28, 2018, two days after the federal judge ordered reunification of families, an email circulated advising Refugee Resettlement affiliates that Health and Human Services was designing a database to “eliminate the need to track information [on families] on spreadsheets.”

At the same time, Refugee Resettlement managers were told, “Please do not wait for the database to go live to initiate contact with parents!”

Homeland Security databases on parents — some on their way to deportation — had no information on whether children had been separated from them. The Homeland Security and Health and Human Services databases were not linked.

As separations ramped up, documents provided to Public Integrity show, Refugee Resettlement staff also began sending more “significant incident reports” about separated migrant children to Homeland Security’s Office for Civil Rights and Civil Liberties.

The Public Integrity and NPR investigation found that during the first half of last year, Refugee Resettlement filed the majority of more than 800 family separation complaints logged by Homeland Security’s civil rights office. Among children who languished in shelters without the office’s help were blind or deaf children — disabled children the civil rights office acknowledges it has authority to expeditiously assist.

Meanwhile, fallout from the mass separations of families continues.

On Nov. 5, a federal judge in Los Angeles ruled that the U.S. government should be held accountable for the impact of the zero tolerance policy. The government, the judge said, must provide mental-health services to thousands of traumatized migrant children who languished without seeing or being in contact with their parents, sometimes for months.