The Justice Department late Friday asked a federal appeals court to allow prosecutors to resume examining the roughly 100 documents marked classified that were recovered in the extraordinary search last month of former President Donald Trump’s Mar-a-Lago home and to bar a special master from reviewing them.

The department told the 11th Circuit U.S. Court of Appeals in Atlanta that a judge’s order temporarily stopping prosecutors from reviewing the documents marked classified “impedes the government’s efforts to protect the nation’s security” and hinders its ongoing investigation into the government records at the former president’s sprawling resort.

Prosecutors asked the appeals court to immediately lift the hold and let them resume their work.

The request comes after U.S. District Judge Aileen Cannon on Thursday appointed a former chief federal judge to independently review the documents. But over the objection of prosecutors, she included the roughly 100 documents marked classified that were recovered in the search and ordered the Justice Department to provide Mr. Trump’s legal team with access to those materials.

FBI agents searched Mr. Trump’s Florida resort on Aug. 8 and removed 33 boxes with thousands of presidential records and news clippings mixed with classified materials. Afterward, prosecutors said they were investigating, among other issues, potential violations of the Espionage Act, which relates to the misuse of classified information.

Restricting federal agents’ access to the documents “unduly interferes” with that ongoing investigation, prosecutors wrote Friday.

Prosecutors argued in their 29-page filing Friday that Mr. Trump had no right to those sensitive national security documents and that the classified markings “establish on the face of the documents that they are not Plaintiff’s personal property.”

The Justice Department lawyers didn’t ask the appeals court to stop the appointment of the special master, Raymond J. Dearie, who was a longtime judge in federal court in Brooklyn, though they said Judge Cannon erred in her “unprecedented” order.

In a request the filing described as “modest but critically important,” the Justice Department asked that the 100 or so documents in question to be excluded from Mr. Dearie’s review process, which Judge Cannon ordered to be completed by Nov. 30. A separate court filing Friday showed Mr. Dearie asked Mr. Trump’s team and Justice Department lawyers to appear for their first conference on Tuesday.

Mr. Trump’s legal team has disputed the status of the documents marked as classified. A spokesman didn’t immediately respond to a request for comment Friday night.

“The government has not proven these records remain classified. That issue is to be determined later,” Mr. Trump’s lawyers wrote in a Monday filing to Judge Cannon.

Mr. Trump has called the Aug. 8 search prosecutorial misconduct and an attempt to keep him from running for president in 2024.

U.S. District Judge Aileen Cannon appointed a former chief judge to independently review classified documents found in Mar-a-Lago.

Photo: Senate Judiciary Committee

When the Florida-based Judge Cannon ordered the appointment of an independent arbiter last week, she had temporarily blocked criminal investigators from using the materials, describing it as “a brief pause to allow for neutral, third-party review to ensure a just process with adequate safeguards.”

The Justice Department said Friday in its motion that it also needed to proceed quickly in its investigation because materials at Mar-a-Lago “were stored in an unsecure manner over a prolonged period, and the court’s injunction itself prevents the government from even beginning to take necessary steps to determine whether improper disclosures might have occurred or may still occur.”

It added that the “government’s need to proceed apace is heightened where, as here, it has reason to believe that obstructive acts may impede its investigation.”

Prosecutors have said they believed efforts were likely taken to obstruct their probe, with documents being removed from a Mar-a-Lago storage room and concealed from investigators who sought them, and obstruction of justice was among the potential crimes under investigation that were listed in the FBI’s warrant to search the premises.

In her Thursday order, Judge Cannon told prosecutors to provide Mr. Trump’s legal team with copies of the classified documents, which legal experts said was highly unusual. The Justice Department in its motion said Mr. Trump’s lawyers were potential witnesses in the criminal investigation and that sharing such information with them could compromise the probe.

“The district court here ordered disclosure of highly sensitive material to a special master and to Plaintiff’s counsel—potentially including witnesses to relevant events—in the midst of an investigation, where no charges have been brought,” the Justice Department said. “Because that review serves no possible value, there is no basis for disclosing such sensitive information.”

It is unclear when the appeals court will make a decision on the Justice Department’s motion.

Write to Sadie Gurman at sadie.gurman@wsj.com, Jan Wolfe at jan.wolfe@wsj.com and Aruna Viswanatha at Aruna.Viswanatha@wsj.com