NEW YORK (Reuters) - The U.S. government may have separated “thousands” more immigrant children from their parents than previously known but inadequate record-keeping means the exact number is still unclear, an internal watchdog said on Thursday.

The Office of Inspector General at the U.S. Department of Health and Human Services (HHS) said the agency had identified many more children in addition to the 2,737 included as part of a class action lawsuit challenging family separations brought by the American Civil Liberties Union (ACLU) last year.

The administration of President Donald Trump implemented a ‘zero tolerance’ policy to criminally prosecute and jail all illegal border crossers even those traveling with their children, leading to a wave of separations last year. The policy sparked outrage when it became public, and the backlash led Trump to sign an executive order reversing course on June 20, 2018.

But the auditor said in a report that prior to the officially announced ‘zero tolerance’ policy, the government began ramping up separations in 2017 for other reasons related to a child’s safety and well-being, including separating parents with criminal records or lack of proper documents.

The report also said more than 100 minors, including more than two dozen under five years old, were separated after the President’s executive order.

Katie Waldman, a spokeswoman for U.S. Department of Homeland Security (DHS) said the practice of separating apprehended minors from adults to protect the interests of the children has been standard practice “for more than a decade.”

Reuters reported in June that from October 2016 through February 2018, before the official ‘zero tolerance’ policy was in place, nearly 1,800 immigrant families were separated at the U.S.-Mexico border.

These separations, though, were only tracked informally, making it impossible for the auditor to know the exact number overall.

The Office of Refugee Resettlement (ORR), which is run by HHS and is responsible for the care of immigrant children, initially recorded separated minors in an Excel spreadsheet and later a database program. “However, use of these tools was not formalized in procedures, and access was limited,” the auditor said.

FILE PHOTO: Immigrant children are led by staff in single file between tents at a detention facility next to the Mexican border in Tornillo, Texas, U.S., June 18, 2018. REUTERS/Mike Blake/File Photo

ORR said in an statement that the agency “has only limited resources,” and that counting prior DHS separations would take away from its main focus of caring for children in government custody. It said it has modified its case management process to interview children at intake and flag cases where there are signs of separation.

The government was ordered to reunite the more than 2,700 families covered by the ACLU lawsuit and report back about the progress of those reunifications regularly to a federal district court in California, including the status of around 400 parents that were deported without their children.

But little is known about the fate of the potentially thousands of children who were released but not covered by the class action, the auditor said. Legally the length of time immigrant children can be held in detention is limited and the government is charged with finding adequate sponsors or care for children who cross the border alone or are separated.

“ORR was unable to provide a more precise estimate or specific information about these children’s placements,” for example if they were placed with relatives or in foster care.

Lee Gelernt, the lead attorney in the ACLU case said in a statement: “We will be back in court over this latest revelation.”

Congressional Democrats said they have already started investigating the issue and plan to hold oversight hearings.

SEPARATIONS CONTINUE

Separations have also continued since Trump’s June executive order ending ‘zero tolerance.’ At least 118 children were separated between July 1 and Nov. 7, 2018, 82 of them were under the age of 13 and 27 of them under the age of 5, according to the report.

Of those, 65 were separated because the parents had a criminal history but in some cases the agency did not provide the details of that history. Other reasons cited included a parent’s gang affiliation, illness or hospitalization or an adult claiming to be a legal guardian of a child without proof.

Anthony Enriquez, director of the unaccompanied minors program at Catholic Charities in New York, said his agency is representing dozens of children who were separated from their parents after June last year.

He said there seems to be no standard for information sharing between the agencies, even months after the government was ordered to reunite many of the families by a court.

“These children are constantly asking, ‘Where is my parent?’,” he said.

The auditor raised concerns that the government is still not adequately counting separation cases.

“It is not yet clear whether recent changes to ORR’s systems and processes are sufficient to ensure consistent and accurate data about separated children,” the report said.