The panel’s decision removed a major obstacle to the Justice Department’s investigation into Mr. Trump’s handling of sensitive government documents.

WASHINGTON — A federal appeals court on Thursday removed a major obstacle to the criminal investigation into former President Donald J. Trump’s hoarding of government documents, ending an outside review of thousands of records the F.B.I. seized from his home and freeing the Justice Department to use them in its inquiry.

In a unanimous but unsigned 21-page ruling, a three-member panel of the U.S. Court of Appeals for the 11th Circuit in Atlanta shut down a lawsuit brought by Mr. Trump that has, for nearly three months, slowed the inquiry into whether he illegally kept national security records at his Mar-a-Lago residence and obstructed the government’s efforts to retrieve them.

The appeals court was sharply critical of the decision in September by Judge Aileen M. Cannon, a Trump appointee who sits in the Southern District of Florida, to intervene in the case. The court said Judge Cannon never had legitimate jurisdiction to order the review or bar investigators from using the files, and that there was no justification for treating Mr. Trump differently from any other target of a search warrant.

“It is indeed extraordinary for a warrant to be executed at the home of a former president — but not in a way that affects our legal analysis or otherwise gives the judiciary license to interfere in an ongoing investigation,” the court wrote.

Limits on when courts can interfere with a criminal investigation “apply no matter who the government is investigating,” it added. “To create a special exception here would defy our nation’s foundational principle that our law applies ‘to all, without regard to numbers, wealth or rank.’”

The panel’s ruling is set to take effect next Thursday. If there is no stay for an appeal before then, the review by the independent arbiter, or special master — Raymond J. Dearie, a judge who sits in the Eastern District of New York — would abruptly end. At that point, Judge Cannon would also be required to dismiss Mr. Trump’s lawsuit.

It was unclear whether Mr. Trump would appeal the appeals court’s decision. Lawyers for the former president did not immediately respond to a request for comment.

Mr. Trump had already asked the Supreme Court to overturn an earlier ruling by the appeals court that excluded 103 documents marked as classified from Judge Cannon’s review, but the justices rejected his request without any noted dissents.

All three of the judges on the panel that ruled on Thursday were appointees of Republican presidents — and two of them, Andrew L. Brasher and Britt Grant, had been placed on the bench by Mr. Trump himself.

The decision came shortly after the chief federal judge of the Federal District Court in Washington ruled that the two top lawyers in Mr. Trump’s White House, Pat A. Cipollone and Patrick F. Philbin, must testify before a grand jury investigating Mr. Trump’s role in an array of efforts to overturn the 2020 election, according to a person familiar with the matter.

Mr. Trump faces legal jeopardy on multiple fronts, even as he begins a third bid for the White House. A special counsel, Jack Smith, is now overseeing two of the most prominent inquiries, one into Mr. Trump’s bid to cling to power after the 2020 election and the documents investigation. A Justice Department spokesman declined to comment.

The appeals court’s ruling on Thursday was not a surprise. During a hearing on Nov. 22, a panel of the court indicated its deep skepticism of the legality of the unusual intervention by Judge Cannon.

“The law is clear,” the appeals court wrote on Thursday. “We cannot write a rule that allows any subject of a search warrant to block government investigations after the execution of the warrant. Nor can we write a rule that allows only former presidents to do so.”

The ruling was an embarrassing development for Judge Cannon, a young jurist who found herself in the middle of a politically sensitive case.

She had not yet served two years on the bench when, in September, she shocked legal experts — and the government — by temporarily barring the Justice Department from using any of the seized materials in its investigation of Mr. Trump and installing a special master to review them and recommend how she should rule on the status of any documents the government and Mr. Trump’s lawyers could not agree on.

Judge Cannon’s appointment of Judge Dearie was especially unusual because she gave him the power to sift through the documents not only for those protected by attorney-client privilege, which is fairly common, but also to evaluate claims by Mr. Trump that some were protected by executive privilege.

There is no precedent for a current or former president to successfully invoke executive privilege to keep the Justice Department — a part of the executive branch — from viewing executive branch materials in a criminal investigation. The appeals court ruling did not reach that issue, however, since it ended Judge Cannon’s review on jurisdictional grounds.

During the early stages of the special master review, Mr. Trump’s lawyers asserted that he personally owned significant numbers of documents that the government said were public property under the Presidential Records Act. Those documents included dossiers about applicants for clemency that Mr. Trump received as president.

The appeals court said it was not considering or endorsing that theory. It said only that even if Mr. Trump could assert ownership over large numbers of the files, it did not mean he could demand their return at this stage of the investigation or that Judge Cannon had jurisdiction to adjudicate such a claim.

Shortly after Judge Cannon’s initial order came down, prosecutors asked the 11th Circuit, based in Atlanta, to reverse it and restore their ability to examine some of the most sensitive documents: a batch of about 100 that were marked as classified. The prosecutors said they needed quick and unfettered access to those materials to fully understand the potential hazards Mr. Trump had caused in storing them at Mar-a-Lago.

Within a week, the appeals court ruled in favor of the government. In its decision, the appellate panel — which included the same two Trump-appointed judges who issued the ruling on Thursday — indicated that it thought that Judge Cannon had committed a basic error and should not have gotten involved in the case at all.

Mr. Trump appealed this early ruling to the Supreme Court, which declined to block it in a terse order with no dissents. Not long after, the Justice Department returned to the 11th Circuit yet again and this time asked the court to shut down the special master’s review altogether.

The ruling on Thursday did precisely that, cutting short Judge Dearie's work before he even completed his review of the materials. During his brief tenure as a special master, Judge Dearie, expressed skepticism about claims by Mr. Trump’s lawyers that the documents he was examining were in fact privileged and thus could be withheld from the Justice Department’s investigation.

In recent weeks, several witnesses connected to the investigation have appeared in front of a grand jury in Federal District Court in Washington. On Thursday, that included three close aides to Mr. Trump, according to two people familiar with the matter.

The aides were Dan Scavino Jr., Mr. Trump’s former social media guru, William Russell and William B. Harrison, who worked for Mr. Trump when he was in the White House, the people said.