In most cases, government officials have said, border officers who make a decision to remove a child from an accompanying adult do so because there are questions about the child’s welfare, or doubts that the adult is genuinely the child’s parent. In some cases, they said, children are separated even though they are traveling with someone who clearly appears to be an aunt, uncle or sibling. Some children have appeared at the border accompanied by adults who later were determined to be using the child to try to gain entrance to the United States, officials have said.

The new numbers were filed with Judge Dana M. Sabraw of the Federal District Court in San Diego as part of the court’s continuing supervision of the family separation issue. In its motion on Tuesday, the A.C.L.U. asked the judge to clarify a set of standards for such separations that would ensure that children are taken from their parents only when there is evidence that the parent is a genuine danger to the child, or is unfit to provide care.

“The administration is still doing family separation under the guise that they are protecting children from their own parents, even though the criminal history they are citing is either wrong or shockingly minor,” said Lee Gelernt of the A.C.L.U.’s Immigrants’ Rights Project. “This is just circumventing the court’s order.”

Children who were separated from their families over the last year spent an average of 68 days in shelters, according to the motion filed with the court, though four children have been away from their families for more than 300 days.

More than half of those separated — a total of 481 — were under the age of 10 at the time of separation, and 185 children were 5 or younger.