FBI agents retrieved highly-classified information in their raid of Mar-a-Lago last week.
The search was prompted by new evidence that the DOJ had uncovered, the NYT reported.
It included footage of a Mar-a-Lago storage facility that alarmed officials, the report said.
Federal agents were prompted to request a warrant to search Donald Trump's Mar-a-Lago estate after reviewing new footage of a hallway outside a storage facility where classified information was being kept, The New York Times reported.
The Times reported Tuesday that the National Archives and Records Administration, which stores records from past presidential administrations, had contacted Trump's legal team earlier this year after discovering that key documents were missing from the Trump administration's records.
The president's team had handed over several boxes of materials in January. Justice Department then returned to Mar-a-Lago in June to collect several more documents that had been marked as classified, which had not been handed back following the original request.
Having obtained surveillance footage from Mar-a-Lago via a subpoena, agents saw something that alarmed them in recordings of a hallway outside a storage room, The Times reported, citing people familiar with the investigation.
The agents also received evidence from a witness that there was more classified material remaining in the storage room, The Times reported.
The report did not specify what officials saw in the footage.
On August 8, FBI agents searched Mar-a-Lago, retrieving several boxes, which reportedly included highly-classified information about the US' nuclear capability.
The agents were acting on a warrant that was unsealed Friday and showed that they believed Trump may have violated the Espionage Act by keeping hold of the documents after leaving office.
Trump has sought to portray the search as politically motivated, but has shifted his story to claim that the documents kept at Mar-a-Lago had been declassified by him while he was president.
He has claimed that he fully cooperated with the DOJ as it sought to retrieve the documents. But reports indicate that he was given several opportunities to comply with requests to hand back material before the FBI search was conducted.