In a lawsuit brought by the American Civil Liberties Union (ACLU), U.S. Judge Dana Sabraw in San Diego had ordered the government in June to reunite families that had been separated after crossing the U.S.-Mexican border.
But the government failed to meet a Tuesday deadline for reuniting an initial group of children under 5.
It said 46 remained separated because of safety concerns, the deportation of their parents, and other issues.
The government has also said reunifications have been slowed by the need for DNA testing and criminal background checks on parents, and to determine their fitness to care for their children.
That has raised questions how the government can reunite the remaining children, a task the judge has called a “significant undertaking.”
Late Thursday, the ACLU urged the judge to impose timelines to avoid further delays or backsliding.
The ACLU said a lack of information about where and when reunions would happen posed dangers for families. It said that in one case, immigration officials left a reunited mother and 6-month-old daughter at a bus stop late at night.
Concerns are not limited to families with small children.
One mother, Isabela was reunited on Thursday with her 17-year-old daughter in Brownsville, Texas, after 43 days apart.
This followed their arrests for crossing the U.S.-Mexico border, after a more than monthlong journey from El Salvador.
“They took the children from us without any explanation,” said Isabela, who asked that only her first name be used. “I felt I had lost her, that I could not find her.”
Isabela faces a July 26 date in immigration court. “I really hope this sacrifice was worth it,” she said.
Sabraw will consider the next steps for the government at a hearing on Friday at 1 p.m. PDT (2000 GMT) in San Diego.
The Trump administration adopted its family separation policy as part of an effort to discourage illegal immigration. It buckled to intense political pressure and abandoned the policy on June 20.
Reporting by Tom Hals; Editing by Lisa Shumaker and Jonathan Oatis