Infants and toddlers were among the children who were put into foster homes or migrant children shelters, often hundreds or thousands of miles away from where their parents were detained. Under separate policies, the administration also made it difficult for relatives other than the children’s parents to take the children into their own homes.

After a review of internal government tallies, The New York Times found last year that more than 700 migrant children had been separated from their families in the months before the government officially announced the zero-tolerance policy.

On June 26, 2018, a federal judge in San Diego, in response to the A.C.L.U. lawsuit, directed the federal government to halt the separations at the border and to reunite children with their parents. President Trump rescinded the policy that same month.

However, the federal inspectors found that separations have continued to occur: As of November, the report found, Health and Human Services had received at least 118 children who had been separated from their families since the court order.

Officials at the Department of Homeland Security, which oversaw the family separations at the border, have said they have separated families only when necessary, such as when a parent is facing a serious criminal prosecution, or when authorities have reason to believe that the adult accompanying the child is not an appropriate guardian.

“The report vindicates what D.H.S. has long been saying,” said Katie Waldman, a spokeswoman for the department. “For more than a decade it was, and continues to be, standard for apprehended minors to be separated when the adult is not the parent or legal guardian, the child’s safety is at risk, or serious criminal activity by the adult. We are required under the law that Congress passed to send all unaccompanied alien children to H.H.S.”

Ann Maxwell, the Health and Human Services Department’s assistant inspector general for evaluation and inspections, said the separations appeared to have been occurring for a full year before the court issued its order.