The department said "government records were likely concealed and removed" from a storage room even after the former president's representatives had assured officials that they had thoroughly searched the property.
The FBI also seized 33 boxes containing more than 100 classified records during its August 8 search of Mar-a-Lago and found three classified documents stashed in office drawers, according to a filing.
It included a photo showing the cover pages of a smattering of paperclip-bound classified documents - some marked as "TOP SECRET//SCI" with bright yellow borders, and one marked as "SECRET//SCI" with a rust-coloured border - along with whited-out pages, splayed out on a carpet at Mar-a-Lago.
Beside them sat a cardboard box filled with gold-framed pictures, including a Time Magazine cover.
The filing shows how investigators conducting a criminal probe have focused not just on why the records were improperly stored there, but also on the question of whether the Trump team intentionally misled them about the continued, and unlawful, presence of government secrets.
The document sheds new details on the events of this past May and June, when FBI and Justice Department officials issued a subpoena for the missing records and then visited a storage room at Mar-a-Lago that contained top-secret documents and other information.
During that June visit, the document says, Mr Trump's lawyers told investigators that all the records that had come from the White House were stored in one location - a Mar-a-Lago storage room - and that "there were no other records stored in any private office space or other location at the premises and that all available boxes were searched".
After that, though, the Justice Department "developed evidence that government records were likely concealed and removed from the storage room and that efforts were likely taken to obstruct the government's investigation".
In their search earlier this month, agents found classified documents both in the storage room as well as in the former president's office, including three classified documents found not in boxes, but in office desks.
The filing responds to a request from Mr Trump's legal team for a special master to review the documents seized during the August 8 search of Mar-a-Lago. US District Judge Aileen Cannon is set to hear arguments on the matter.
Mr Trump's lawyers last week asked for the appointment of a special master who would be tasked with reviewing the records taken and setting aside documents protected by claims of legal privilege. Ms Cannon on Saturday said it was her "preliminary intent" to appoint such a person but also gave the Justice Department an opportunity to respond.
On Monday, the department said it had already completed its review of potentially privileged documents and identified a "limited set of materials that potentially contain attorney-client privileged information".
In a separate development, the Trump legal team has grown with the addition of another attorney. Chris Kise, Florida's former solicitor general, has joined the team of lawyers representing Mr Trump, according to two people familiar with the matter who were not authorised to discuss the move by name and spoke on condition of anonymity.
Mr Kise did not return messages seeking comment.