Washington (CNN) Migrant children who were separated from their parents as part of the Trump administration's controversial "zero tolerance" policy last year experienced "heightened feelings of anxiety and loss," caregivers from US government shelters told the Health and Human Services inspector general.

A report released Wednesday includes accounts of facility staff detailing the inconsolable crying of children when they were separated, the kids' confusion and belief they had been abandoned by their parents.

As a result of the policy and longer stays in government custody, facility staff faced challenges in meeting the mental health needs of children, many of whom had already experienced significant trauma before arriving to the United States.

"Every single separated kid has been terrified. We're [seen as] the enemy," a program director says in the report, noting that separated children couldn't tell the difference between facility staff and immigration agents.

The report provides yet another snapshot of how the Trump administration's policy of separating families at the US-Mexico border affected children -- this time, from some of the staff tasked with caring for them. The policy, which ended last June , resulted in the separation of thousands of families.

"According to program directors and mental health clinicians, separated children exhibited more fear, feelings of abandonment, and post-traumatic stress than did children who were not separated," according to the report, which reviewed the mental health needs of children in HHS custody.

"Children who did not understand why they were separated from their parents suffered elevated levels of mental distress," the report says.

Staffers explained the behavior of separated children in detail.

"Some separated children expressed acute grief that caused them to cry inconsolably," the report states, adding that others "who believed their parents had abandoned them were angry and confused."

"A 7-or-8-year-old boy was separated from his father, without any explanation as to why the separation occurred," one program director told the inspector general. "The child was under the delusion that his father had been killed and believed that he would also be killed."

The "psychological pain" also manifested into physical symptoms, according to a medical director included in the report: "You get a lot of 'my chest hurts,' even though everything is fine [medically]. Children describe symptoms, 'Every heartbeat hurts,' 'I can't feel my heart,' of emotional pain."

Toll on children

Immigrant advocacy groups, doctors, and lawyers have repeatedly raised concern over how the policy was handled and the toll it took on children. In congressional testimony earlier this year, Dr. Julie Linton, testifying on behalf of the American Academy of Pediatrics, reiterated that family separation "can cause irreparable harm" on children, and "carry lifelong consequences for children."

Democratic lawmakers have also slammed Trump administration officials over the policy, frequently questioning them in congressional hearings about whether the impact on the children was taken into consideration.

The Office of Refugee Resettlement, an agency within the Health and Human Services Department, is tasked with the care of unaccompanied migrant children, including addressing their mental health needs.

The mental health care of children in custody is particularly important given the significant trauma some experience in their home countries or on the journey to the United States. In one case, detailed in the report, "a medical coordinator reported that a girl had been held in captivity for months, during which time she was tortured, raped, and became pregnant."

Other children, according to the report, had witnessed the rape or murder of relatives.

The inspector general visited 45 Office of Refugee Resettlement-funded facilities nationwide in August and September 2018, speaking with approximately 100 mental health clinicians, as well as medical coordinators, facility leadership, and federal field specialists.

The Office of Refugee Resettlement was caring for around 12,400 children during the time of the IG's review. The majority of the children were from the Northern Triangle countries of Guatemala, Honduras, and El Salvador.

The report found that facilities faced challenges in meeting the mental health needs of children who had experienced significant trauma; employing in-house mental health clinicians and preparing them to treat children with intense trauma; accessing external providers to treat children who need a higher level of care; and transferring children who needed specialized treatment.

Impact of longer stays

Policy changes in 2018, like the administration's controversial "zero tolerance" policy, exacerbated the issues faced by facilities.

The increase in children age 12 or younger, for example, presented difficulties to staff who typically served teenagers.

"The little ones don't know how to express what they are feeling, what has happened. Communication is limited and difficult. They need more attention," a program director is included as saying in the report.

Another policy of requiring fingerprint checks for all adult members of a sponsor's household when the sponsor applies to take in unaccompanied minors also led to children staying in custody longer. Immigrant advocates said at the time that the fingerprinting policy, which was reversed in December , stoked fear among the undocumented community and may have kept some sponsors from coming forward.

Care provider facilities reported that longer stays "resulted in deteriorating mental health for some children and increased demands on staff," the report states.

"According to facility staff, longer stays resulted in higher levels of defiance, hopelessness, and frustration among children, along with more instances of self-harm and suicidal ideation," reads the report.

"One mental health clinician, for example, remarked that even children who come into care with good coping skills become disillusioned after a lengthy stay," it adds.

The Administration for Children and Families, of which ORR is part, concurred with the recommendations laid out in the report.

"ACF is equally committed to providing the public with a fair accounting of ORR program operations. To that end, we agree with OIG that significant factors beyond ACF's control contributed to the issues identified in this report," the agency said in a response included with the report.

The recommendations include working with subject matter experts to identify and provide tools to help staff, minimize time in ORR custody, and ensuring that ORR's "national network of external healthcare providers includes the mental health specialists needed to address children's mental health needs." ACF concurred with the recommendations and is working on efforts to address them, according to a response included in the report.

Review of required checks of employees

In a separate report released Wednesday , the HHS inspector general reviewed whether required employee background checks were completed at ORR-funded facilities, looked at whether case managers and mental health clinicians met the minimum requirements, and assessed staffing challenges.

The report found that generally, facilities met background checks and qualification requirements, but in some instances, facilities didn't have evidence of some checks or allowed staff to begin working before receiving the results of the FBI fingerprint check or the Child Protective Services check or both.

Given the direct access to children in these facilities, background investigations are required for "all prospective staff, contractors, and volunteers," and checks must be completed before being hired, the report states.

"The failure of some facilities to complete required background checks prior to allowing employees direct access to children may have placed the health and safety of some children at risk," Amy Frontz, assistant inspector general for audit services, said in a call with reporters Wednesday.

The IG also noted in the report that six facilities were granted a waiver from conducting the check for employees with access to children. Under certain circumstances, ORR is permitted to "waive or modify sections of the background investigation regulation" for an influx facility, meaning facilities that are temporarily used to accommodate a surge in children arrivals.

This story has been updated.