NEW YORK (CBSNewYork/AP) — Dozens of immigrant children will be released from detention centers and reunited with their parents Tuesday.

The court-ordered deadline to reunite all immigrant parents and children younger than 5 years old was imposed by a federal judge in a case brought by the ACLU.

A government lawyer said Monday at least 54 children would join their parents by the deadline, only about half of the 100 or so children covered by the order. The Trump administration was working on final background checks for another five children ahead of Tuesday’s deadline.

The Justice Department said at least 44 children will remain in custody because a parent has been deported, faces criminal charges or can’t be found.

The government is also facing a July 26 deadline for the rest of the 3,000 minors separated from a parent at the border.

On Monday, a federal judge in Los Angeles rejected the Trump administration’s efforts to detain immigrant families in long-term facilities, calling it a “cynical attempt to undo a longstanding court settlement.”

U.S. District Judge Dolly Gee said the government had failed to present new evidence to support revising a court order that limits the detention of children who crossed the border illegally.

The two sides revealed in a filing late Monday that they are far apart on protocols for reunification, with the government arguing its practices are necessary under federal law to ensure child safety and the ACLU contending that many are too cumbersome under the circumstances.

One area of disagreement is DNA testing on parents and children, with the government saying it should be the general rule and the ACLU saying it should be done only when no other evidence is available to prove parentage.

(© Copyright 2018 CBS Broadcasting Inc. All Rights Reserved. The Associated Press contributed to this report.)