The Justice Department checked with the White House before informing a federal judge that it was already carrying out part of President Obama’s immigration amnesty, administration attorneys revealed in documents filed in court late last week as they tried to head off a judicial spanking.

The attorneys turned over the communications with the White House to Judge Andrew S. Hanen, who is hearing the major case challenging Mr. Obama’s 2014 deportation amnesty, but the lawyers pleaded with the court not to look at the documents on grounds that it would intrude on the president’s powers.

Still, the revelation that the White House was looped in suggests officials knew the seriousness of the error in not informing Judge Hanen earlier that the Homeland Security Department was already carrying out part of Mr. Obama’s amnesty by granting three-year work permits to illegal immigrants who qualified under the 2012 policy.

“The Department of Justice and the White House counsel’s office sometimes confer regarding civil litigation that impacts high-priority policy initiatives of the administration,” the attorneys said in a 34-page brief filed Friday that repeatedly apologized for misleading the court, while insisting it wasn’t intentional.

In documents filed with the court, the attorneys said more than 1,500 Homeland Security employees knew the three-year part of the amnesty was in effect as of November.

The Justice Department attorneys are trying to avoid a reprimand from Judge Hanen, who has expressed surprise that the administration was carrying out any part of the amnesty, despite telling him in both filings and during a hearing that the amnesty program wouldn’t begin until February.

Judge Hanen issued an injunction blocking the full amnesty on Feb. 16, two days before it was to take effect. The administration two weeks later informed the judge that it already was carrying out a part of the amnesty.

“We sincerely regret the misunderstanding that the government’s statements inadvertently caused, and hope that this submission fully resolves the issue,” the administration said in its brief.

Texas Attorney General Ken Paxton, who is leading the challenge against Mr. Obama’s amnesty, said the government failed to turn over anything of value and was ignoring the court’s orders.

“Not only does the Obama administration deny the coalition of 26 suing states the opportunity to review documents about how the DOJ misrepresented the early implementation of its executive amnesty program, it also suggests that the judge himself should not review those documents,” Mr. Paxton said. “Regardless, we will continue to fight for the rule of law by asking the district court to carefully review the administration’s withheld documents and hold the DOJ accountable so they provide reliable information about this case, both to the court and to the states.”

Texas has asked for limited discovery in the case to try to figure out how seriously it should treat the government’s behavior. Judge Hanen now has those documents and will have to decide what to make public.

The fight is over one small part of the series of actions Mr. Obama announced in November when he expanded his policies granting deportation amnesty to illegal immigrants.

His 2012 amnesty for so-called Dreamers granted them legal status and work permits good for two years. In November, Mr. Obama expanded the status and eligibility to three years. The court says it wasn’t told about the three-year expansion.

“Whether by ignorance, omission, purposeful misdirection, or because they were misled by their clients, the attorneys for the government misrepresented the facts,” the judge said last month, adding that he was stunned the government waited two weeks after his ruling to inform him that the applications already had been processed.

Texas has argued that had it known applications were being processed, it would have taken extra legal steps to try to halt the program earlier.

Judge Hanen is considering whether to issue sanctions against the Obama administration — though he has said he won’t strike the government’s pleadings, which essentially would have erased the administration’s defense and granted victory by default to Texas. Judge Hanen said that while that may have been warranted, it would be a disservice to the weighty issues at stake in the case, including fundamental issues of presidential power.

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