The ACLU said late Sunday the administration provided it with a list of 102 children under 5 years old and that "appears likely that less than half will be reunited" by Tuesday's deadline.
Also, on Monday, a federal judge in Los Angeles emphatically rejected the Trump administration's efforts to detain immigrant families for an extended period.
Federal officials told reporters Tuesday that immigrant parents being reunited with their children are instead being outfitted with ankle monitors and released from custody.
"This is real progress, I'm optimistic that many of these families will be reunited tomorrow", he told the courtroom.
Handout/Reuters Baby and toddler high chairs are seen at the Bristow facility, in this photo provided by the U.S. Department of Health and Human Services, in Bristow, Virginia.
In the meantime, many of these children have had to face their immigration proceedings without their parents in court. At Tuesday's hearing, he said the process is taking too long and needs to be "streamlined". Eleven of those adults had serious criminal histories, the statement said, including "charges or convictions" for child cruelty, kidnapping, murder, human smuggling or domestic violence. They will be set free in the United States pending the outcome of their immigration cases, which can take several years. One adult had a falsified birth certificate, one was accused of abusing the child who had been brought across the border, one was being treated for "a communicable disease" and one had planned to house their child with an adult who had been charged with child sexual abuse.
"The seriousness of the crimes is the reason why we are not going to reunite them", said Matthew Albence of Immigration and Customs Enforcement, of the 22 cases.
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On June 26 - just days after Trump had signed an executive order terminating the policy - Sabraw ruled in the ACLU's favor, officially triggering the beginning of the reunification process. Health and Human Services manages their care inside the USA, while Homeland Security has control over adults in immigration detention, and the Justice Department manages the immigration courts.
If the government failed to reunite all the children under 5 with their parents by Thursday, Sabraw asked the ACLU to suggest penalties he could levy against the government.
According to court filings, both children were forcibly taken from their parents at the border and brought to Noank Community Support Services in CT, where they are now being cared for. "Can they at some point get their children back?"
HHS and DHS are working to make arrangements for those children ages 5 to 17, officials said.
In this June 25 photo, a mother migrating from Honduras holds her 1-year-old child while surrendering to U.S. Border Patrol agents after illegally crossing the border, near McAllen, Texas. Children spend an average of 57 days in shelters before they're placed with a sponsor.
DOJ lawyers said in a court filing that the government has tried for twelve months to locate the parents, to no avail. They are given access to medical care and counselling, as well as school.
The lead-up to the Monday court appointment indicated the duress the Trump administration is now under in trying to swiftly reunite the families it has separated - and just how messy the situation has gotten.
A different judge, in Los Angeles, on Monday dismissed as "dubious" and "unconvincing" the U.S. Justice Department's proposal to modify a 1997 settlement known as the Flores Agreement, which says that children can not be held in detention for long periods, irrespective of whether they're with their families.