WASHINGTON — The Trump administration said Thursday all eligible small children separated from their families as a result of its zero-tolerance immigration policy have been reunited with their parents.

But nearly half of the children under 5 remain separated from their families because of safety concerns, the deportation of their parents and other issues, the administration said.

The administration was under a court mandate to reunify families separated between early May and June 20, when President Donald Trump signed an executive order that stopped separations.

The American Civil Liberties Union filed a lawsuit on behalf of a woman who had been separated from her child, and U.S. District Court Judge Dana Sabraw ordered all children reunited with their parents.

Fifty-seven children were reunified with their parents as of Thursday morning, administration officials said.

“Throughout the reunification process, our goal has been the well-being of the children and returning them to a safe environment,” according to a statement  from the heads of the three agencies responsible for the process.

The officials said 46 of the children were not eligible to be reunited with their parents; a dozen parents had already been deported and were being contacted by the administration.

In 22 other cases, adults posed safety concerns, they said.

The 46 children will remain in the care of Health and Human Services, which will continue to seek to place them with a sponsor, such as other family members or even foster care, as it does for the more than 10,000 other minors who arrived in the U.S. without a relative.

Children spend an average of 57 days in shelters before they’re placed with a sponsor. They are given access to medical care and counseling, as well as school.

The zero-tolerance policy calls for the criminal prosecution of anyone caught crossing the border illegally. Because parents can’t take their children to jail, they were separated.

At least 2,300 children were separated from about 2,200 adults until the executive order was signed.

The administration faces a second, bigger deadline — July 26 — to reunite more than 2,000 older children with their families.