The agency claimed in a court document that “efforts were probably made to hinder the government’s investigation.”
The document was sent in response to Mr. Trump’s lawsuit seeking the appointment of a “special master” to oversee a portion of the ongoing litigation.
Mr. Trump asserted that the materials were declassified while denying any misconduct.
In the filing released on Tuesday, the Justice Department’s counterintelligence chief, Jay Bratt, gives the clearest picture so far of the department’s attempts to retrieve documents from the former president.
Those attempts led to a National Archives team visiting his Mar-a-Lago home in January, an FBI team visiting in June, and the FBI searching the mansion on 8 August.
US presidents must transfer all of their documents and emails to the National Archives.
Who visited Mar-a-Lago, when, and why?
In January, the National Archives retrieved 15 boxes of White House records from Mar-a-Lago, where they found highly classified records were “unfoldered” and “intermixed with other records” – some pages had been torn up.
Upon learning the boxes contained “highly classified reports”, the Justice Department and the FBI began investigations which found evidence that “dozens of additional boxes” likely containing classified information still remained at his property.
On 3 June, three FBI agents and a DOJ attorney arrived at Mar-a-Lago to collect materials. According to Mr Trump’s lawyers, he told them:Â “Whatever you need, just let us know.”
But agents were “explicitly prohibited” by his representatives from searching any boxes inside a storage room at Mr Trump’s property, according to the latest filing.
Evidence was also found that the records were “likely concealed and removed” from the storage and that efforts were “likely taken” to obstruct the investigation, officials said.
Following the June visit, FBI teams searched Mr Trump’s property again in August – where they found over a hundred classified documents.
This was twice as many classified documents found “in a matter of hours” than by the “diligent search” that Mr Trump’s team claimed they had previously carried out.
Mr Bratt said that this “casts doubt on the extent of cooperation in this matter”.
At the time, Mr Trump rejected reports he had mishandled official records as “fake news”.
Mr Trump’s lawyers have asked that a “neutral” third-party attorney – known as a special master – be brought in to determine whether the seized files are covered by executive privilege, which allows presidents to keep certain communications under wraps.
But the latest court filing said that any presidential records seized in the search warrant “belong to the United States, not to the former president”.