A migrant child holds the hand of a Lutheran Social Services worker helping to reunite children separated from their parents, on July 26, 2018. (Matt York/AP)

A government report released Thursday said the Trump administration probably separated thousands more migrant children from their parents at the U.S. border than has previously been made public, but federal efforts to track those children have been so poor that the precise number is unknown.

The report issued by the inspector general for the Department of Health and Human Services says no one systematically kept count of separated children until a lawsuit last spring triggered by the Trump administration’s “zero tolerance” policy, under which the government tried to criminally prosecute all parents who crossed the border illegally, taking their children from them in the process.

As a result of the lawsuit, the government identified about 2,700 separated children in federal custody as of June, some of them infants and toddlers.

But Health and Human Services officials say there was a sharp spike in separated children starting nearly a year earlier, shortly after President Trump took office, the report said. Investigators now say thousands more children were taken from their parents or other guardians by border or immigration agents during that time and later released.

The report said that estimate was based on “informal tracking” by the HHS office responsible for refu­gee children and did not include more specific numbers.

As a result of the lawsuit, the government began tracking separated children more closely. An additional 118 children were taken from their parents from July to November, the report said, in most cases because immigration enforcement officials said the adults had criminal histories or other issues.

Although previous administrations also separated minors at the border in some instances — usually when they suspected the child was smuggled, or if the parent appeared unfit — the report said the practice appears far more common under Trump and began nearly a year before administration officials publicly acknowledged it.

Separated children accounted for 0.3 percent of all unaccompanied minors taken into HHS ­custody in late 2016, near the end of the Obama administration, ­investigators found. By August 2017, the percentage had increased more than tenfold, to 3.6 percent.

The government’s announcement in May that it was significantly increasing separations because of the zero-tolerance policy triggered an international uproar, prompting Trump to halt the practice in late June.

The American Civil Liberties Union, which sued the government over the separations, said the report released Thursday “reaffirms that the government never had a clear picture of how many children it ripped from their parents. . . . We will be back in court over this latest revelation.”

A spokeswoman for the Department of Homeland Security pushed back against the finding that thousands of additional migrant children had been separated, saying the report did not provide a solid basis for that figure.

Spokeswoman Katie Waldman said, however, that the report “vindicates” the department’s contention that the federal government has been separating children from parents with criminal records or other evidence that they posed a danger for many years.

HHS spokeswoman Evelyn Stauffer said the report illustrates “the herculean work” done by staff in the Office of Refugee Resettlement, part of the department’s Administration for Children and Families, to figure out which children in its care had been separated and reunify them with their parents.

Stauffer noted that investigators had found “no evidence whatsoever suggesting that [the refu­gee office] lost track of children in its care” — a reference to allegations last year triggered by reports that some sponsors did not respond to inquiries from government officials after minors were released to their custody.

The 24-page report by the HHS internal watchdog gives new insight in particular into the time before and after the court order that resulted from the ACLU lawsuit, which required HHS officials to carefully track the status of separated children and submit reports to a federal judge.

It also draws fresh attention to flawed data systems and poor communication between federal agencies, which left HHS officials uncertain this summer which of the minors in their custody had been separated.

Asked Thursday whether those systems are now adequate, Ann Maxwell, an assistant HHS inspector general, told reporters, “The jury is still out on that.

In a separate interview, Maxwell said the informal tracking by health officials consisted at first of a spreadsheet kept by the refu­gee office and later an online document to which field staff could make additions if they heard anecdotally from the contract facilities about children who had been separated.

The report is the first in a series of “issue briefs” the inspector general’s office is planning this year to shed light on the system of care in which tens of thousands of minors apprehended at the border are housed in a network of private facilities run by contractors and scattered around the country.

The shelters serve as way stations for the youngsters while the refu­gee office and caseworkers look for potential sponsors — usually adult relatives — they can live with as they await immigration hearings.

Later reports will focus on background checks and other screening of staff hired at the facilities, their response to incidents in which children are harmed, and their ability to provide appropriate medical and mental health care.

The overwhelming majority of minors in HHS custody cross the border on their own, but the agency also takes charge of children whom the government separates from their parents.

According to the report, the most common reason the Department of Homeland Security gave health officials for the 118 most recent separations was that parents had a criminal history. But information on the parents’ criminal records often was so sketchy, the report said, that it is unclear whether the separations were warranted or whether the children could be safely returned to their parents. When the refu­gee office sought more information, the report said, DHS officials “did not always respond.”

Last fall, the DHS produced an unpublished report documenting the chaos triggered by the family separations.

Among other things, the report found that 860 migrant children were kept in Border Patrol holding cells longer than three days and that inadequate steps were taken to track the identities of children too young to talk.