More than 2,000 children were separated from their parents by USA immigration authorities at the border this spring before Trump reversed course on June 20 amid an worldwide outcry.
In Tuesday's filing, administration lawyers stated that a remaining 27 children were not eligible for reunification with a parent and were therefore not subject to the court-mandated reunification deadline.
Under the "zero-tolerance", policy, while parents entering the USA illegally were held for prosecution, children were placed in Department of Health and Human Services (HSS) facilities across the country.
One there is no information on the parent. The ACLU would like a faster reunification process while the USA government claims they are bound by strict protocols, such as a plan to DNA test every child and parent before a reunification can occur.
"ICE will take custody and then release the parent and child together", Fabian said at Monday's hearing.
The civil liberties organization said in a statement Tuesday night that "while the government is now attempting to comply with the court orders, it's failing because of real logistical problems, like missing records or parents whose locations it failed to track".
Lee Gelernt, the ACLU lawyer handling the case, said the government is taking the reunification demands seriously, though he said he thinks the government can do better than the 54.
The administration faces a second, bigger deadline - July 26 - to reunite perhaps 2,000 or so older children who were also separated from their families at the border in the past few months.
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In court in San Diego, Sabraw said DNA tests to determine if a child belongs to a family aren't necessary if family members have other documentation, such as a birth certificate.
Also Monday, a federal judge in California sharply rebuked the Justice Department for seeking a modification to a long-standing court settlement. While parents are held in jail to await trial by a judge, children are moved into accommodation managed by an HHS agency.
U.S. Border Patrol agents take a father and son from Honduras into custody near the U.S. -Mexico border, June 12, 2018, near Mission, Texas.
"My take on this whole situation is we're not done yet", she said. The families will be released after they are reunited. But the government does not have the room: Immigration and Customs Enforcement has three family detention centers with space for 3,000 people, and they are already at or near capacity, though the Trump administration is trying to line up space at military bases.
Two weeks have passed since President Donald Trump signed an executive order to end his administration's policy of separating undocumented immigrant children and parents, but chaos still reigns at the border and across the country as family reunification has hit roadblocks. An additional 20 children have purported parents with whom they can not be reunited because those adults have already been either removed from the United States or released into the country, which removes DHS and HHS's ability to force them to come get the children they claim are theirs. 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.
The American Civil Liberties Union received the list of the names of the almost 100 children under the age of 5 who were separated from their parents at the border, according to a group spokesman.
In total, the authorities are holding around 11,800 minors who crossed the border illegally.