WASHINGTON—A special Justice Department team has withheld from investigators some of the documents seized earlier this month from former President Donald Trump’s Mar-a-Lago home because they might include information protected by attorney-client privilege, the department said Monday.

The disclosure came in a brief court filing, which said the agency had already finished reviewing those potentially privileged materials, a development that could render partly duplicative a federal judge’s preliminary decision to appoint an outside party known as a special master to review the seized documents.

On Saturday, U.S. District Judge Aileen Cannon signaled she intended to name such a special master to review the materials, which Mr. Trump’s lawyers had requested two weeks after the Aug. 8 search.

In an Aug. 22 motion, Mr. Trump’s legal team called the FBI search a “shockingly aggressive move,” and asked that someone outside the Justice Department be appointed to examine the documents to “preserve the sanctity of executive communications and other privileged materials.” The team also asked the judge to order investigators to immediately stop examining the items.

A special master is a third party, usually a retired judge, given the task of reviewing evidence and filtering out irrelevant materials or communications protected by attorney-client privilege, executive privilege or similar legal doctrines.

The Justice Department is expected to respond in more detail on Tuesday to Mr. Trump’s request, which cited issues beyond attorney-client privilege. Judge Cannon scheduled a hearing for Thursday for arguments on the matter.

In the Monday filing, prosecutors said the department already had set up a separate filter team to review the documents for potentially privileged information before agents on the investigation examined them. That initial review team identified “a limited set of materials that potentially contain attorney-client privileged information,” completed its review of those documents, and was in the process of addressing potential issues with the material, the filing said.

According to a property receipt released after the search, FBI agents removed around two dozen boxes from Mar-a-Lago, including 11 sets of classified documents. The document didn’t specify how many documents in total agents seized.

A separate document released Friday, the heavily redacted affidavit which described the Federal Bureau of Investigation’s justification for its search of the Florida estate, outlined how law-enforcement officers not involved in the investigation would search Mr. Trump’s Mar-a-Lago office. The affidavit referred to it as “45 Office”—an apparent reference to Mr. Trump being the 45th president—and said the separate team would identify and separate out any documents that might be covered by attorney-client privilege.

Judge Cannon had also ordered the Justice Department to file under seal a more detailed receipt showing what property it seized; prosecutors are expected to file that on Tuesday.

The Monday filing also noted that the Justice Department and the Office of the Director of National Intelligence are facilitating a “classification review” of the seized materials, and that U.S. intelligence agencies are conducting an assessment of the risk to national security that would result from the materials being disclosed.

Director of National Intelligence Avril Haines told lawmakers last week that the intelligence agencies would undertake that assessment.

On Monday, White House press secretary

Karine Jean-Pierre declined to say whether President Biden would be briefed upon completion of the damage assessment. The White House said Mr. Biden wasn’t briefed in advance about the search of Mar-a-Lago but won’t discuss whether the concern about sensitive documents reached his desk in the form of his daily briefing.

“It is something I can’t even speak to,” Ms. Jean-Pierre said, noting the briefings are classified.

—Alex Leary contributed to this article.

Write to Aruna Viswanatha at Aruna.Viswanatha@wsj.com