A senior Justice Department official recently told Donald Trump’s legal team that law-enforcement officials don’t believe the former president returned all of the government documents he took with him when he left the White House, people familiar with the matter said.

The communication from Jay Bratt, chief of the Department of Justice’s counterintelligence and export-control section, was the latest indication that the government is still seeking some records it believes Mr. Trump should have relinquished at the end of his administration.

The National Archives and Records Administration told Congress late last month that it hadn’t recovered all of the presidential records that were supposed to be turned over, adding that there was “no easy way to establish absolute accountability.”

The Justice Department declined to comment on Mr. Bratt’s outreach, which was reported earlier by the New York Times. Mr. Trump’s spokesman, Taylor Budowich, in a statement didn’t address the substance of the communication between the government and the former president’s lawyers.

Mr. Budowich said a “weaponized Department of Justice and the politicized FBI are spending millions and millions of American tax dollars to perpetuate witch hunt after witch hunt.”

The FBI seized roughly 11,000 documents during its Aug. 8 search of Mr. Trump’s Mar-a-Lago home in Florida, an extraordinary move that came after Mr. Trump’s team failed to hand over all of the material during several less-invasive attempts to retrieve it earlier this year.

It couldn’t be determined what, if anything, law-enforcement officials planned to do to retrieve the missing information, nor was it clear what the Justice Department believes it has yet to recover.

The Justice Department’s efforts to investigate documents seized at Mr. Trump’s Florida estate have gotten bogged down in a legal battle between the former president and the federal government. A federal judge last month appointed a retired judge, known as a special master, to review independently the documents the FBI seized.

The department recently scored a set of wins when an appeals court said it could resume reviewing roughly 100 documents marked as classified, and later agreed to fast-track its appeal of a broader ruling, trying to challenge U.S. District Judge Aileen Cannon’s decision to halt the criminal investigation for months so the special master could review evidence.

Mr. Trump’s team this week asked the Supreme Court to intervene and provide the special master with the sensitive documents. Justice Clarence Thomas,

who received the petition, gave the Justice Department a week to file a brief in response.

In one of the boxes found in Mr. Trump’s office at Mar-a-Lago, 99 newspaper and magazine clips dated from 2017 and 2018 were held alongside seven documents marked as top secret, 15 documents marked as secret, 43 empty folders marked as classified and 28 empty folders labeled “Return to Staff Secretary/Miliary [sic] Aide,” among other items, the receipt shows.

Another five empty folders with classified banners were found in the storage room, according to the list. It couldn’t be determined whether the files originally held in any folders marked classified were found elsewhere in the search or have been otherwise accounted for.

Write to Sadie Gurman at sadie.gurman@wsj.com and Alex Leary at alex.leary@wsj.com