Children in custody and their parents are also undergoing DNA cheek swabs, which will take about a week to confirm a match, the US said.
Federal Judge Dana Sabraw ordered the government to reunite children under the age of 5 with their parents by July 10 and all children by July 26.
"We have a vital and historic mission here to protect these children", he said.
The US will return immigrant children under five who were separated from their parents after crossing the Mexican border by July 10 to comply with a court order, Health and Human Services Secretary Alex Azar said Thursday.
But a number of bureaucratic hurdles have complicated the efforts to place those children back with their parents.
In mid-June, the Department of Homeland Security said it separated almost 2,000 children from their parents in April and May after the Department of Justice announced a "zero-tolerance" policy to prosecute everyone who crosses the border illegally.
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Time is running out for the federal government to meet court-imposed deadlines to reunite the thousands of immigrant children who were separated from their parents under the Trump administration's "zero tolerance" policy.
The separation of children as young as 3 from their parents led to protests and public outcry.
The U.S. government attorneys said they may fail to meet those deadlines due to delays in confirming family relationships, but Sabraw declined to extend them without more information.
Azar said on Thursday that HHS "will comply with the artificial deadlines created by the court", but that federal officials are focusing for now on confirming family matches prior to reunification.
About 11,800 minors are now in U.S. custody after crossing over from Mexico, Azar said.
The administration is now also grappling with a series of court-imposed deadlines after a judge ordered the United States government to halt most family separations at the border and the reunification of separated families. "We have not sent children into ICE custody yet, pursuant to the court's order, but we will do so as we approach the court's deadline".
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The judge, who has yet to rule on the extension, said the government needed to provide a full list of those under five held in custody by Saturday afternoon, following which the original deadline would be re-evaluated.
But Homeland Security officials told The New York Times on Thursday that the chaos was exacerbated by the fact that customs agents had deleted certain government records that could have been used to reunite the families.
The Justice Department also asked if the court will permit reunifications outside of the ordered timelines "in cases where parentage can not be confirmed quickly".
Falcon, communications director for RAICES, a nonprofit in Texas that offers free and low-priced legal services to immigrants and refugees, called the move deplorable because collecting such sensitive data would allow the government to conduct surveillance on the children "for the rest of their lives".
Lee Gelernt, deputy director of the ACLU's Immigrants' Rights Project, had this reaction to the action in court on Friday, according to a news release: "The judge made it very clear he wasn't going to allow the Trump administration to drag its feet on reunifying these children with their parents".
The government says it has 16 children under age 5 in its custody who it has not beeen able to link to an adult.
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