WASHINGTON — The Trump administration failed to recognize that 14 children in its care for months had been separated from their families at the Mexican border, officials conceded in a court filing.

The disclosure raises fresh questions about whether the administration neglected to account for additional children after separating them from their parents under its “zero tolerance” immigration policy this spring. Two recent government reports faulted the administration’s tracking efforts, and one said officials feel no obligation to find children who were released to other homes before a judge ordered an accounting of them, suggesting the total separated under the policy may never be known.

Seven of the 14 children’s parents have criminal histories that disqualify them from reunification, officials with the Health and Human Services Department told a federal judge in San Diego. The judge demanded in June that the administration account for every child separated under the enforcement strategy ordered by Attorney General Jeff Sessions.

All of the newly discovered children are 5 years old or older.

The 14 children were part of the more than 2,600 separated from adults at the border before President Trump halted the practice in June in the face of international outrage. But the revelation calls into question the administration’s months of assurances to the judge, lawmakers and the public that it had accounted for every child.

The separations have become a rallying cry for California politicians fighting Trump’s agenda, including Sens. Dianne Feinstein and Kamala Harris. And the issue of what to do with families trying to cross the border is likely to flare up again as a caravan of several thousand Central Americans makes its way north through Mexico.

The 14 additional children were discovered after a review “in light of new information,” which the agency holding the children said it does regularly, according to a status report that Justice Department officials filed late Thursday with U.S. District Judge Dana Sabraw in San Diego.

The news comes after an inspector general’s investigation found discrepancies last month in the government’s data on separated children.

That investigation found that, contrary to public pronouncements, the Department of Homeland Security did not have “a central database” of separated families. It also found differences between Homeland Security numbers for separated children and information that other agencies were using.

Homeland Security “has struggled to provide accurate, complete, reliable data on family separations and reunifications, raising concerns about the accuracy of its reporting,” the Homeland Security inspector general wrote.

The Government Accountability Office issued a report with similar findings Wednesday, saying the administration did not know how many children had passed through its system and felt no obligation to find out.

Administration “officials told us that they do not know how many such children separated from parents at the border were released to sponsors prior to the order and that the court order does not require the department to know this information,” the report said.

The administration has completed 2,104 reunifications and otherwise released or deemed ineligible for reunification another 563 children, according to Thursday’s court filing. Two hundred sixty-four children remain in government custody, the status report said.

Asked about the possibility that the administration may have lost track of additional children, Health and Human Services spokesman Mark Weber said the agency “is taking appropriate action to ensure compliance with the court’s orders, and safe and speedy reunification of separated children with class members.”

The lead attorney for the American Civil Liberties Union, which filed suit over family separations even before the “zero tolerance” policy took effect, said Friday that the administration has bungled its handling of detained children from the start.

“Given the lack of a plan or system to keep track of families, it’s no surprise the original numbers were inaccurate,” said ACLU attorney Lee Gelernt.

All 14 children cited in Thursday’s court filing are still in the custody of Health and Human Services, the administration said. The court filing did not specify what will happen to them. However, for the hundreds of children not on track to be reunified, the only legal alternatives are a relative or close friend in the U.S. who can take them in, long-term foster care or detention until they turn 18.

Judge Sabraw had ordered the government to reunify all eligible separated families by July 26. Reunification has taken longer for hundreds of families, however, because parents were deported or otherwise difficult to track down.

The ACLU says 60 separated children ended up in California shelters. The state’s lawmakers have been outspoken against the separations. Feinstein called the practice a “deeply immoral and haphazard policy that fundamentally betrays American values.” Harris said the practice amounted to “the United States government committing a human rights violation” and called for Homeland Security Secretary Kirstjen Nielsen to resign.

Tal Kopan is The San Francisco Chronicle’s Washington correspondent. Email: tal.kopan@sfchronicle.com