“C.B.P. does not declare that a parent poses danger to a child arbitrarily or without merit,” the agency said in a statement. It said agents “will maintain family unity to the greatest extent operationally feasible,” separating children only in the presence of “a legal requirement” set out in written policy or “an articulable safety or security concern that requires separation.”

But opposition to the new separations has been growing from both outside and inside the federal government. At the Health and Human Services Department’s Office of Refugee Resettlement, which oversees the care of separated children until they can be reunited with their families, some officials have tried to resist receiving children referred to the agency by the Border Patrol.

According to an official who was not authorized to discuss government business and spoke on the condition of anonymity, staff members have in some cases raised questions with Border Patrol agents about separations with what appear to be little or no justification. In some of those cases, border agents have refused to provide additional information, the official said, or if additional documents were provided, they were sometimes redacted to the point of illegibility.

The official, along with another staff member at the Department of Homeland Security, the Border Patrol’s parent agency, said that some separations were occurring with no formal notification to the refugee resettlement office. Both officials said they had been made aware of concerns about an apparent inconsistency in standards applied by border agents when determining whether a family should be separated.

The failure to keep accurate records suggests that more children could have been separated than the 245 accounted for by Feb. 20 in official records.

The New York Times reviewed several cases of children who have been separated since the policy was officially ended, and learned of many others through the lawyers who handled them. Some of the new separations, the review showed, occurred in families with a parent who had a drunken-driving conviction in the past, or a 20-year-old nonviolent robbery conviction. In one case, a parent had been convicted of possession of a small amount of marijuana.

Donna Abbott, vice president for refugee and immigrant services at Bethany Christian Services, a contractor that accommodates migrant children in temporary foster homes until they can be reunited with family members, said most cases of family separations do not list detailed reasons, making it difficult to evaluate whether they were appropriate.