Sessions on June 25 said they would continue to prosecute adults who enter the United States illegally.
The administration said another 46 children under the age of five remain separated from their families because of safety concerns and other issues. Justice Department attorneys have been under a 6 p.m. ET Thursday deadline to explain to Dana Sabraw, the US district judge behind the court order, how they returned the eligible children - and why the rest are ineligible for return under the court's guidelines. The parent of one child has simply disappeared.
Sabraw then asked the American Civil Liberties Union - which is representing the plaintiffs in a lawsuit against the Trump administration - to suggest a potential punishment if the government fails to meet the deadline. It should be transparent and easy to do.
However, 46 of the initial group of 103 children "were acknowledged by the court to be ineligible for reunification".
The Trump administration said all eligible children under five taken from their parents because of zero-tolerance immigration policies have reunited with their mothers or fathers.
The government said that brief delays were because it was still completing its screening process, which government officials have noted detected some individuals who were not the parents or were not eligible for reunification.
In the filing, Chris Meekins, chief of staff of HHS's Office of Preparedness and Response, said he was concerned the truncated process will put children at risk. They said they had to conduct DNA tests on all parents and children to ensure that they were indeed related, and had to conduct background checks on parents to ensure that children weren't being handed over to criminals. At least three of the adults who were not parents were blood relatives, however - two grandmothers and an uncle.
"Throughout the reunification process, our goal has been the well-being of the children and returning them to a safe environment", according to a statement from the Departments of Health and Human Services, Homeland Security and Justice.
Locals stay away from protests near Donald Trump's prized possession
Trump will depart Britain Friday for Finland to prepare for a summit with Russian President Vladimir Putin Monday in Helsinki. Protests coinciding with Mr Trump's visit are set to take place in Glasgow this evening and in Edinburgh on Saturday.
The administration is facing an even more daunting court-ordered deadline to reunite about 2,000 older children with their parents by July 26.
The government has cited logistical issues in getting some of them back together (one being that some parents were already deported). According to the court filing, the mother called an attorney and an immigration advocacy group for help, and finally secured a bus ticket around midnight on Tuesday.
But almost half of the children under 5 remain apart from their families because of safety concerns, the deportation of their parents and other issues, the administration said.
The families will be released from custody with an ankle monitor and orders to appear before an immigration judge for further hearings, a U.S. Immigration and Customs Enforcement official said. Fabian said those decisions were handled at the field level, adding that HHS, which houses the detained children, had limited resources. A Honduran man strangled himself after officials took his son, and Republicans and Democrats alike criticized the policy.
Meanwhile, some reunions of older children are happening around the country.
The Trump administration has emphasized that immigrants who want to claim asylum should do so at ports of entry instead of trying to come in illegally.
A recent opinion poll suggests there is public support for detaining families, even among Americans who opposed family separations.
In Friday's court filing, officials argued that when preparing for reunifications for children under 5, their background checks raised some red flags, including adults who were found not to be parents and some criminal concerns, like an adult in a home who had been accused of sexually abusing a young girl. The government initially identified 102 children who fell in that category, but the number has fluctuated in recent days, as Sabraw's order has essentially functioned as a judicially mandated audit of the morass of systems used by different federal agencies.