A federal judge on Thursday blocked the Trump administration from deporting Guatemalan children after rejecting the Department of Homeland Security's claim that it was reuniting the youngsters with their parents, who had asked for their return.

In his ruling, Judge Timothy Kelly of the U.S. District Court in the District of Columbia, said the administration's assertion of reuniting children and parents "crumbled like a house of cards" because "there is no evidence before the Court that the parents of these children sought their return" to Guatemala.

The judge temporarily barred the administration from transferring, repatriating, removing or otherwise facilitating the transport of any of the 76 Guatemalan children immigration authorities had tried to deport in the middle of the night over the Labor Day weekend.

Kelly ruled similarly for other Guatemalan children who arrived unaccompanied and are staying in Office of Refugee Resettlement shelters. These children don't have a final order of removal or have not been given permission from the U.S. Attorney General to voluntarily leave the country.

The Trump administration disagreed with the ruling.

"This judge is blocking efforts to REUNIFY CHILDREN with their families. Now these children will have to go to shelters. All just to 'get Trump.' This is disgraceful and immoral," Tricia McLaughlin, Department of Homeland Security assistant secretary, said in an email to NBC News.

The decision follows emergency orders issued Aug. 31 and Sept. 1 by another District of Columbia district judge to prevent the planes loaded with Guatemalan children from departing.

Attorneys for the children had said the federal government notified them in the dead of night that the children were being "repatriated," the ruling states.

The administration had said that it was not violating provisions of the Trafficking Victims Protection Act, which includes various measures protecting unaccompanied migrant children, because they were repatriating and reuniting the children, not deporting and removing them, according to the ruling.

But a report from the attorney general of Guatemala "undermines" the administration's claims, the judge stated.

According to the report, the administration had provided Guatemala a database of 609 adolescents, ages 14 to 17. Only about 50 to 57 parents of those minors, however, were willing to welcome the return of their children and within that small group, "none of them was requesting their [child's] return," Kelly stated in his ruling.

The administration "plunged ahead in the middle of the night with their 'reunification' plan and then represented to a judge that a parent or guardian had requested each child's return, that turned out not to be true," the judge stated.

"Such a rushed, seemingly error-laden operation to send unaccompanied alien children back to their home countries is one of the things that the TVPRA's process prevents," stated Kelly, whom President Donald Trump nominated for the court in 2017.

According to the written ruling, the 76 children placed on planes were "phase one" of a plan to return 327 youngsters to Guatemala.

The 76 included children in foster homes. Although a child in a foster home had told an immigration judge she was scared to return to Guatemala and had no one there to care for her, her foster parents woke her up in the middle of the night over the Labor Day weekend "because immigration was sending her to another place." She was put on a bus and brought to an immigrant shelter," the judge stated.

The late-night attempt to spirit the children out of the country left many traumatized and fearful, according to court documents.

Many migrant children who come to the U.S. on their own have been trafficked or are vulnerable to becoming victims of trafficking, or they have fled abuse or neglect in their home countries. Legal groups that represent many such children have clashed with the administration this year as Trump has sought to deport more immigrants.

The government of Guatemala had expressed concern about children from the country being placed in immigration detention and had said in a diplomatic note that unaccompanied children who return "by judicial action or voluntarily" would be "received safely" for reunification with family, the judge's ruling states.

The administration said it fulfilled Guatemala's request by finding cases of Guatemalan children who were "appropriate for reunification," Kelly stated in his ruling.

Last week, an immigration group added Honduran children to the lawsuit on which Kelly made his ruling, but the temporary halt to deportations was limited to Guatemalan children.

In his previous term as president, Trump's separation of children at the border from parents or guardians -- which resulted in some children remaining in the country while their parents were deported -- drew heavy backlash and criticism from within his own party.

Judge blocks deportation of Guatemalan children