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Lawyers for Donald Trump have argued that the storage of sensitive files at his Florida home "should have never been cause for alarm".
His legal team said the FBI search last month was "unprecedented, unnecessary, and legally unsupported".
Their filing comes on the eve of a court hearing about Mr Trump's call for a third-party official to oversee the evidence taken from Mar-a-Lago.
Officials say the search was necessary due to obstruction by the Trump team.
The 19-page legal filing posted by the former president's team on Wednesday night did not respond to the justice department claims of obstruction.
Upon leaving office, US presidents must transfer all of their documents and emails to the National Archives, which maintains historic White House records.
Mr Trump's legal team contended he had been engaged in a "standard give-and-take" with the National Archives over the return of his files when the search warrant was executed.
"There is no question... that the matters before this court centre around the possession, by a president, of his own presidential records," says the court filing.
His lawyers argue: "The notion that Presidential records would contain sensitive information should have never been cause for alarm."
The court filing came less than 24 hours after the justice department alleged that Mr Trump's aides had probably tried to conceal secret documents inside the West Palm Beach estate.
A National Archives team visited the seafront golf club in January and retrieved 15 boxes of White House records that contained "highly classified reports", said the filing.
The justice department began investigations which found evidence that "dozens of additional boxes" probably containing sensitive material still remained at Mar-a-Lago.
On 3 June, three FBI agents and a justice department lawyer arrived at Mar-a-Lago to collect materials, but were "explicitly prohibited" by Mr Trump's representatives from searching any boxes inside a storage room at the property, according to the 54-page filing.
Evidence was also found that records were "likely concealed and removed" from the storage area and that efforts were "likely taken" to obstruct the investigation, officials said.
On Thursday, a judge will hold a hearing on whether an independent legal official known as a special master should be appointed to oversee the evidence and determine whether any of it is protected under executive privilege - a rule which shields some presidential documents.
The justice department has argued that a special master is not necessary, given that it says most of the evidence has already been inspected by investigators.
In Wednesday's court papers, Mr Trump's lawyers accused the justice department of "gratuitously" including a photograph in its Tuesday filing of "allegedly classified materials" that had been "pulled from a container and spread across the floor for dramatic effect".
"Left unchecked, the DOJ will impugn, leak, and publicize selective aspects of their investigation," Mr Trump's lawyers wrote, arguing why a special master was necessary.
