U.S. District Judge Dana Sabraw in San Diego ordered the government on Monday to submit plans later this week on how it will reunite families still separated after detained at the border in recent months.
The majority of the estimated 2,500 separated children ages 5 to 17 were returned to their parents by last week's court deadline. But hundreds were not.
Officials say the remaining families were ineligible for reunification by the deadline. They include more than 400 children whose parents were deported without them.
Children were taken from their parents as part of President Trump's zero tolerance border enforcement policy. The separations were rescinded following widespread outcry over the practice.