The Department of Homeland Security knew it lacked the technology to track more than 26,000 children it expected to separate from their parents at the U.S. southern border in 2018 as part of its controversial “zero tolerance” policy. As a result, the roughly 3,000-plus children DHS ultimately estimated as being affected may actually be a severe underestimate, the agency’s inspector general reported Wednesday.

“Because of these IT deficiencies, we could not confirm the total number of families DHS separated during the Zero Tolerance period,” the watchdog office said in a report.

[Chad Wolf sworn in as acting DHS chief]

The inspector general found an additional 1,369 potential family relationships that U.S. Customs and Border Protection failed to log and concluded there was a “high risk that DHS did not account for all separated children.”

The findings further illuminate the behind-the-scenes chaos in the lead-up to the rollout this past May of one of the most controversial immigration policies of the Trump era.

Under the “zero tolerance” policy implemented under then-Attorney General Jeff Sessions, thousands of adults crossing the southern border were separated from their children and referred for criminal prosecution. The migrant children were labeled “unaccompanied” and placed in the care of the Health and Human Services Department.

But DHS did not have the required technology or procedures in place to track the families it separated, the inspector general reports. Agency officials first became aware of these issues in 2017 — but did not fully remedy them. One senior CBP official told IG investigators that “key stakeholders had pressured DHS to implement the policy in May” before data and procedural issues had been fixed.

Once the policy went into effect, CBP officials logged separations in an existing database in an ad-hoc manner without the ability to properly document details of “zero tolerance” cases separately from the others. The IG report noted that in one case, an Arizona-based nonprofit had inquired about a deaf minor who had been separated from his father, but the child’s case record did not contain details of his separation or disability.

“This process was neither easy nor accurate,” the authors of the IG report wrote, adding that the officers “immediately struggled to keep pace with the high volume of migrant apprehensions and separations.”

Around 82 percent of the adults separated from their children ultimately got minimal or no jail time, and promptly returned to CBP custody. Yet, in 2,000 cases in which parents returned with time-served sentences, or without being prosecuted at all, CBP did not immediately reunite them with their children. Detention facilities, therefore, became overcrowded and separations continued, according to the report.

On June 20, President Donald Trump issued an executive order directing that families be detained together. Soon after, a federal judge issued a ruling against family separations and ordered affected children be reunited with their parents.

DHS estimates around 2,100 children were reunited as a result, although the OIG questioned that figure because of various recordkeeping deficiencies.

In a letter responding to a draft of the report, a DHS official concurred with some aspects of the IG report, but argued that the draft included “inflated numbers that will lead to misunderstandings and misperceptions” of the agency’s effort to comply with court orders.

The numbers have “undergone rigorous double and triple line-by-line checking by the relevant agencies,” DHS said in its response.

Rep. Carolyn B. Maloney, the New York Democrat who chairs the Oversight and Reform Committee, said the report illustrates the Trump administration’s “cruelty, incompetence, and indifference to the suffering of children” affected by the zero-tolerance policy.

“Previous independent reports showed that the Administration failed to track these children, and now we know why — a rush to execute a callous and unnecessary policy and a willful blindness to known problems,” she said in a statement.

The policy, although only in effect as originally intended for six weeks, did not achieve its stated goal of ending “catch-and-release,” the practice of releasing migrants who have crossed the border from government custody while they await trial, the inspector general found. Instead, it ended up further burdening resources at the agency: The tracking deficiencies alone cost the agency 28,000 hours and $1.2 million in staff overtime.