SAN DIEGO/WILMINGTON, Del. (Reuters) - The U.S. government is struggling to reunite immigrant families it separated at the border with Mexico and only about half the children under age 5 will be back with their parents by a court-ordered deadline of Tuesday, a government attorney told a judge on Monday.

U.S. Judge Dana Sabraw in San Diego last month ordered the government to reunite the approximately 100 children under the age of 5 by Tuesday, and the estimated 2,000 older children by July 26.

Sarah Fabian, an attorney with the U.S. Department of Justice, said 54 children younger than 5 would be reunited with parents by the end of Tuesday, and the number could increase depending on background checks.

The other parents have either been deported, failed a criminal background check, were unable to prove they were the parent or had been released and immigration agents had been unable to contact them, said Fabian.

The children were separated under U.S. President Donald Trump’s “zero tolerance” policy that called for the prosecution of immigrants crossing the border illegally. The separations were in place from early May until Trump stopped the practice last month in the face of intense criticism.

Trump made cracking down on illegal immigration a key part of his presidential campaign in 2016.

The judge directed the government to file a detailed accounting of the reunification process and scheduled a hearing for Tuesday at 11 a.m. PDT (1800 GMT).

Lee Gelernt, an attorney for the American Civil Liberties Union, which brought the case, said he did not think the government was complying with the reunification order.

“It is very troubling that there are children and parents who are not in some kind of government tracking system,” he said after the court hearing. He added that nonprofit groups were trying to find parents the government had failed to locate, who are mostly from El Salvador, Guatemala and Honduras.

He also questioned if the government’s list of children under the age of 5 was accurate.

Gelernt added, however, that he believed the government had made “significant” steps in the past 48 hours to unite parents with their children, and he called the effort “a blueprint for going forward with the remaining more than 2,000 families.”

Fabian told the judge that once parents and children were reunited, they would likely be released from immigration custody. A legal settlement dating from the 1990s only allows the government to detain children in adult centers for a brief period.

Gelernt said the ACLU was concerned that parents would be put on the street without any money in an unfamiliar city.

The organization and government agreed the locations of the releases would not be disclosed, and the government agreed to work with immigration advocates to ensure the parents had money for a hotel and other necessities.