The group said the administration provided it with a list of 102 children under 5 years old who must be reunited by Tuesday under an order by U.S. District Judge Dana Sabraw in San Diego.
It was the first time the government indicated whether the parents and children would be released or detained together. After reunification, they face a series of other obstacles - including long, complex legal proceedings, and possibly deportation. Some families are only partially reunified; a child may be returned to his mother, for instance, while his father remains in detention.
"The objective of the [Trafficking Victims Protection Act ] is to promote the best interests of the child and to reunite families", the ACLU had argued.
He scheduled another hearing for Tuesday morning to get further updates on the reunifications, which he ordered as part of a class-action lawsuit filed by the ACLU. "We just don't know how much effort the government's made to find" the parents. It said in a statement that it "appears likely that less than half will be reunited" by that deadline.
These provisions included DNA testing and background checks on unrelated people who might end up living in the same home as the reunited family. Another parent planned to live in a household with an adult who had an outstanding warrant for sexual abuse of a child and can not be reunited unless they identify a different place to live, according to the filing.
ICE has three family detention centers with room for about 3,000 people in all, and the places are already at or near capacity.
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Mr Basu said detectives will continue with their "painstaking and meticulous work to gather all the available evidence". Hours later, emergency workers responded to the same address after the 45-year-old man had fallen ill, police said.
We are going to propose within 48 hours of contacting a parent who is in the USA, and within one week of contacting a parent who's already been removed to another country. The numbers were revealed during a court hearing between the government and the American Civil Liberties Union, which secured Sabraw's preliminary injunction requiring family reunification last month.
In a seven-page order, the judge called that request "a cynical attempt, on an ex parte basis, to shift responsibility to the judiciary for over 20 years of congressional inaction and ill-considered executive action that have led to the current stalemate".
Devin O'Malley, a Justice Department spokesman, said the department disagreed with Gee's Monday ruling and continued to review it. If the parent is actually in criminal custody now, reunification can not occur.
Now the family detention system is at capacity - as are a network of about 100 shelters for migrant minors who traveled into the US without parents or a guardian and who now wait anywhere from a few weeks to years to have their cases resolved in the immigration courts. Fabian said, arguing their hands are tied by logistics.
Among the other remaining question marks is whether authorities can streamline their vetting process for the migrant parents - which ACLU attorneys have described as needlessly cumbersome - and whether the government can pass along the locations migrant families will be released from custody, so that charity groups can more quickly offer them support.
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.