WASHINGTON — The Justice Department asked a federal judge on Thursday to revisit her decision to temporarily stop prosecutors from gaining access to classified documents seized from former President Donald J. Trump’s Florida home, arguing that her ruling was hindering the government’s effort to determine whether national security had been compromised.
In a pair of filings in federal court, lawyers for the department announced their intention to appeal key parts of Judge Aileen M. Cannon’s ruling. They said they would ask an appeals court to block those sections of her order if she does not agree to do so herself by next Thursday.
Judge Cannon’s order, issued on Monday, has prevented the department from using the documents, some marked as highly classified, in its investigation into Mr. Trump’s handling of sensitive government documents.
In the ruling, she said she planned to appoint an independent arbiter, known as a special master, to sift through the more than 11,000 documents and 1,800 other items the F.B.I. seized during a court-authorized search last month of Mr. Trump’s property, Mar-a-Lago. The special master would also be authorized to identify and set aside any materials potentially protected by attorney-client or executive privilege — or that were of a clearly personal nature.
Prosecutors asked Judge Cannon to allow investigators to continue to use “classified records — a discrete set of just over 100 documents” and to withhold them from the special master.
The department, in forceful and foreboding language, argued that determining the national security implications of Mr. Trump’s retention of the documents was so intertwined with its criminal investigation that carrying out a separate risk assessment was impossible under the conditions imposed by the court.
Justice Department lawyers complained that the judge’s order was impeding efforts to determine whether there may yet be “additional classified records that are not being properly stored” and noted that the search had recovered empty folders marked as classified whose contents “may have been lost or compromised.”
In an order on Thursday evening, Judge Cannon directed Mr. Trump’s lawyers to respond to the government’s filing by Monday.
In an affidavit accompanying the filing, Alan E. Kohler Jr., the assistant director of the F.B.I.’s counterintelligence division, wrote that the intelligence community’s assessment of the classified material was “inextricably linked with the criminal investigation.”
More on the Trump Documents Inquiry
Department lawyers wrote that “uncertainty regarding the bounds of the court’s order and its implications for the activities of the F.B.I. has caused the intelligence community, in consultation with D.O.J., to pause temporarily this critically important work.”
The government and the public, the department added, “are irreparably injured when a criminal investigation of matters involving risks to national security” is frozen or delayed.
The department did not contest appointing a special master to sift through documents and photographs not marked as classified. Nor did it challenge Judge Cannon’s order preventing investigators from working with those files until they were cleared by the special master, although it said it disagreed with that part of her decision, too.
Instead, prosecutors asked Judge Cannon to grant them immediate access only to the classified material, arguing that her ruling had been based on concerns about Mr. Trump’s personal materials — including medical and financial records — that were swept up in the search.
“The classification markings establish on the face of the documents that they are government records, not plaintiff’s personal records,” they said.
Prosecutors added that Mr. Trump has no right to have classified government documents returned to him and there is no plausible claim that any are subject to attorney-client privilege.
And while they conceded that some classified documents might arguably be subject to executive privilege, they argued that criminal investigators would be entitled to have access to them anyway. Under a 1974 ruling, the Supreme Court allowed the Watergate prosecutor to obtain President Richard M. Nixon’s Oval Office tapes even though he had tried to invoke the privilege.
Mr. Trump has claimed that he had declassified everything he removed from the Oval Office to his residence. But his lawyers have not made that same assertion in the courtroom, where there are professional consequences for lying.
Instead, they have agreed that it would be appropriate for the special master to have a top secret security clearance. If Judge Cannon ultimately decides to limit the special master to reviewing those documents not marked as classified, the arbiter would not need a clearance, expanding the pool of potential candidates.
None of the three criminal laws cited as the basis of the search, including the unauthorized retention of national security secrets and obstruction of justice, require the documents to have been deemed classified.
In her ruling, Judge Cannon left open the possibility that Mr. Trump’s legal team could contest the seizure of some materials based on an assertion of executive privilege.
But the department noted in its filing that Mr. Trump “himself declined to assert any claim of executive privilege over the classified records” found at Mar-a-Lago after a grand jury issued a subpoena for them in May.
The government is still required to confer with Mr. Trump’s lawyers to produce a list of potential arbiters to the court by Friday, unless the judge extends the deadline she imposed this week. A spokesman for the department said it intended to do so, provided it could reach an agreement with Mr. Trump’s team.
The filing said the government would soon make available to Mr. Trump’s team “copies of all unclassified documents recovered during the search — both personal records and government records.” It added that it would return Mr. Trump’s personal items that were not mixed with classified records.
Mr. Trump’s legal team did not immediately comment on the filing.
But on his Truth Social platform, Mr. Trump accused the department of planting evidence and complained about its decision to appeal the ruling. He called Judge Cannon, whom he appointed in November 2020, “a brilliant and courageous judge whose words of wisdom rang true throughout our nation.”
Under Judge Cannon’s ruling, prosecutors are barred from using the trove of documents they retrieved in the search of Mar-a-Lago for further investigation pending the completion of a review by the arbiter.
Her order allowed the intelligence agencies to continue assessing the potential risks to national security caused by the insecure storage of highly classified documents at Mr. Trump’s private club and residence.
Thursday’s filing was an attempt to place the onus back on Judge Cannon.
The submission of the filing, including the declaration that Judge Cannon’s order was creating national security problems, also added to the factual record the government could put before the appeals court.
Notably, the government did not file a motion to reconsider, a formal request for the judge to reverse her ruling. Such motions are notoriously hard to win, in part because they essentially ask judges to acknowledge they were wrong in making an earlier decision.
The appointment of a special master is more likely to delay than derail the investigation into Mr. Trump’s handling of highly classified documents. Yet the legal and constitutional stakes are high.
Attorney General Merrick B. Garland and other senior department officials have been wrestling with the dilemma of whether to let the order stand to speed up the process, or to appeal a ruling they believe is wrong about the law and should be reversed — at the cost of potentially longer delays.
Advisers to Mr. Trump are already proceeding as if the appointment of the special master were an accomplished fact and have begun considering several potential candidates who would be acceptable to the court, including former judges, according to a person familiar with the situation.
In a separate action on Thursday, the Justice Department obtained permission from a federal judge in Washington to disclose more information about subpoenas that were issued this summer to the Trump Organization for documents marked as classified and surveillance camera footage at Mar-a-Lago. Mr. Trump’s legal team has already acknowledged the existence of the subpoenas in litigation.
At the time, prosecutors were trying to use a grand jury subpoena to retrieve the remaining documents marked as classified at Mar-a-Lago. They were also seeking to determine whether any materials had been removed from a storage closet at the property and wanted the footage to see who had access to the room.
Those subpoenas were mentioned in the affidavit used to obtain the warrant to search Mar-a-Lago. The Justice Department is seeking to release parts of that affidavit that had been redacted in an earlier disclosure, but it first needs permission from the magistrate judge in Florida who signed the warrant.
Maggie Haberman contributed reporting.