The FBI searched Donald Trump’s Mar-a-Lago resort in Florida after it obtained evidence there was probably an effort to conceal classified documents in defiance of a grand jury subpoena and despite his lawyers suggesting otherwise, the justice department said in a court filing.

The recounting – contained in a filing from the justice department that opposed Trump’s request to get an independent review of materials seized from Mar-a-Lago – amounted to the most detailed picture of potential obstruction of justice outlined to date by the government.

“Efforts were likely taken to obstruct the government’s investigation,” the justice department alleged in its filing on Tuesday night.

Among the new revelations in the 36-page filing were that FBI agents recovered three classified documents from desks inside Trump’s office at Mar-a-Lago and additional classified files from a storage room, contrary to what the former president’s lawyers indicated to the justice department.

The justice department said in the submission that, after a Trump lawyer in May accepted service of a subpoena for materials removed from the White House, the lawyer and Trump’s records custodian in June gave the government a single Redweld legal envelope, double-taped, that contained the documents.

As Trump’s lawyer and custodian turned over the folder to Jay Bratt, the justice department’s chief counterintelligence official, the custodian produced and signed a letter certifying a “diligent search” had been conducted and all documents responsive to the subpoena were being returned.

The lawyer for the former president also stated to Bratt that all the records in the envelope had come from one storage room at Mar-a-Lago, that there were no other records elsewhere at the resort, and that all boxes of materials brought from the White House had been searched, the justice department said.

The custodian who signed the letter has been identified by two sources familiar with the matter as Christina Bobb, a member of Trump’s in-house counsel team, though a copy of the letter reproduced by the justice department in the filing redacted the custodian’s name.

But the FBI subsequently uncovered evidence through multiple sources that classified documents remained at Mar-a-Lago in defiance of the subpoena, and that other government records were “likely” concealed and removed from the storage room, according to the filing.

The justice department said in its submission that the evidence – details of which were redacted in the search warrant affidavit partially unsealed last week – allowed it to obtain a warrant to enter Mar-a-Lago, where FBI agents found more classified documents in Trump’s private office.

“The government seized 33 items of evidence, mostly boxes,” from its search of Trump’s resort in Palm Beach, Florida, the filing said. “Three classified documents that were not located in boxes, but rather were located in the desks in the ‘45 Office’, were also seized.”

Illustrating the contents of the 8 August seizure, in an exhibit resembling how the justice department would show the results of a drug bust, the filing included a photo of the retrieved documents emblazoned with classification markings including “top secret” and “secret” designations.

The justice department added that the documents collected most recently by the FBI included materials marked as “sensitive compartmented information”, while other documents were so sensitive that the FBI counterintelligence agents reviewing the materials needed additional security clearances.

“That the FBI,” the filing said, “recovered twice as many documents with classification markings as the ‘diligent search’ that the former president’s counsel and other representatives had weeks to perform, calls into serious question the representations made in the June 3 certification.”

After painting an extraordinary portrait of the hurdles that the justice department had to overcome to even recover the documents that belong to the government, prosecutors argued that Trump had no basis to seek the appointment of a so-called special master to review the files.

The request for a special master in this case fails, the filing argued, because Trump is attempting to use the potential for executive privilege to withhold documents from the executive branch – which the supreme court decided in Nixon v GSA did not hold.

The justice department added that even if Trump could somehow successfully assert executive privilege, it would not apply to the current case because the documents marked classified were seized as part of a criminal investigation into the very handling of the documents themselves.

Trump is expected to press on with his request for a special master and to obtain a more detailed list of materials taken from Mar-a-Lago, according to a source close to his legal team, which also disputed that the justice department’s filing raised the likelihood for an obstruction charge.

On Tuesday morning, before the justice department filed its response minutes before a court-imposed midnight deadline, Trump added a third lawyer, the former Florida solicitor general Christopher Kise, to his outside legal team, said two sources with direct knowledge of the matter.