Donald Trump retained documents bearing classification markings, along with communications from after his presidency, according to court filings describing the materials seized by the FBI as part of the ongoing criminal investigation into whether he mishandled national security information.

The former US president kept in the desk drawer of his office at the Mar-a-Lago property one document marked “secret” and one marked “confidential” alongside three communications from a book author, a religious leader and a pollster, dated after he departed the White House.

The mixed records could amount to evidence that Trump wilfully retained documents marked classified when he was no longer president as the justice department investigates unauthorised possession of national security materials, concealment of government records, and obstruction.

The classification status of the two documents is in dispute after Trump claimed that all documents at Mar-a-Lago had been declassified before he left office, though no such evidence has emerged and his lawyers have not repeated it in court.

New details about the commingled documents came in a eight-page filing submitted by the justice department on Saturday to Raymond Dearie, the special master examining whether the 103 documents seized by the FBI should be excluded from the evidence cache.

The justice department said towards the end of the filing: “Because plaintiff [Trump] can only have received the documents bearing classification markings in his capacity as president, the entire mixed document is a presidential record.”

The commingled records appear to have some significance to the criminal investigation, since the two classified documents were the only ones found in Trump’s office besides those contained in a leather-bound box and one additional document that the FBI seized during its search on 8 August.

The leather-bound box contained some of the most sensitive records found at Mar-a-Lago: seven documents marked “top secret”, 15 marked “secret”, two marked “confidential”, as well as 45 empty folders with “classfied” banners and 28 folders marked “Return to Staff Secretary/Military Aide”.

Trump has attacked the investigation as a partisan effort designed to hurt him politically, as analysts speculate he will announce his 2024 campaign on Tuesday.

The Guardian identified the nature and location of the commingled documents at issue by comparing the unique identifier numbers with a spreadsheet filed by the justice department showing they were part of “Item #4” seized by the FBI, which is described in another filing as “Documents from Office”.

The documents investigation is expected to intensify in the coming weeks, with the midterm elections largely finished and federal investigators closing in on several key witnesses.

The justice department gained testimony last Friday from top Trump adviser Kash Patel about claims that all the documents seized from Mar-a-Lago were declassified, after he was forced to take limited immunity and appear before a federal grand jury in Washington.

It comes after federal investigators also obtained contradictory accounts from Walt Nauta, a former White House valet who followed Trump to Florida after his presidency, about removing boxes from a storage room at Mar-a-Lago that was used to keep some documents marked classified.

The justice department has also attempted in recent weeks to compel Trump to return more government documents that it believes to be in his possession, prompting some of Trump’s lawyers to discuss ideas such as having an outside firm certify that no more records remain, say people close to the matter.