By Tal Kopan and Ariane de Vogue, CNN

(CNN) -- Another federal judge has overruled the Trump administration's efforts to end a popular immigration program -- this time saying the government has to accept new applications.

The ruling on the Deferred Action for Childhood Arrivals program, however, won't take immediate effect, with the judge delaying the ruling for 90 days to allow the administration to make its case in a new memo justifying the end of the program.

Similar to the other rulings, Judge John Bates concluded that the wind-down of DACA was "arbitrary and capricious" because the Department of Homeland Security failed to "adequately explain its conclusion that the program was unlawful." The judge also accused the government of providing "meager legal reasoning" to support its decision.

A George W. Bush appointee to the US District Court for the District of Columbia, Bates delayed the implementation of his ruling "to allow the agency an opportunity to better explain its rescission."

In response to the ruling, the Justice Department said it stands by its original reasoning, calling DACA an "unlawful circumvention of Congress," and that it intends to continue making its case to the courts.

"The Department of Homeland Security therefore acted within its lawful authority in deciding to wind down DACA in an orderly manner," spokesman Devin O'Malley said in a statement. "Promoting and enforcing the rule of law is vital to protecting a nation, its borders, and its citizens. The Justice Department will continue to vigorously defend this position, and looks forward to vindicating its position in further litigation."

In his 60-page decision, Bates took the administration to task for its justification for ending DACA, which was almost entirely based on a threat from Texas and a handful of other states to challenge DACA in court.

Bates called the move "particularly egregious" given the hundreds of thousands of DACA recipients, young undocumented immigrants who came to the US as children, protected under the program over its five years. Given how many people's lives were built on the protections from DACA, Bates said, "its barebones legal interpretation was doubly insufficient."

Bates concluded that the argument that a Texas court would have likely immediately halted the program "was so implausible that it fails even under the deferential arbitrary and capricious standard."

The DACA program has already been resumed after President Donald Trump sought to end it in September, after two federal judges issued nationwide rulings to accept renewals of the two-year permits issued by the program and after the Supreme Court declined to circumvent the appeals process to overturn those decisions.

But while the DHS has been processing renewal applications under those rulings, as the appeals make their way through the courts, Tuesday's ruling was the first to order the program to resume accepting new applications -- potentially opening the program to tens of thousands more immigrants than the roughly 700,000 currently protected.

In September, the administration defended ending the program by saying it was likely to fall in the courts anyway, arguing a six-month wind-down of the program would be more orderly than a sudden end brought by the courts. No court has found DACA to be unconstitutional.