He is suing federal Special Minister of State Don Farrell and National Anti-Corruption Commissioner Paul Brereton over allegations of mistreatment.
Anti-corruption officials searched the 31-year-old's home in June 2024 over allegations he misappropriated secret documents related to French submarines five years earlier.
They were searching for sensitive documents on the since-abandoned submarine project Lehrmann was alleged to have stolen from the office of former defence minister Linda Reynolds.
The 31-year-old has denied the allegations and sought assistance from the federal government to cover the legal costs of his defence.
During the search, NACC officials seized two diaries, one red and one blue.
Lawyers for the anti-corruption watchdog say the blue diary may contain security-classified information, in the latest twist in the former staffer's legal proceedings.
Lehrmann wants the diary back, but the government has indicated it may apply to withhold part or all of it based on whether its contents are sensitive or relevant to the lawsuit.
On Wednesday, Lehrmann's lawyer Zali Burrows also said her client was not notified when NACC distributed the diary to the home affairs and defence departments.
"The horse has bolted," she told the Federal Court.
"It's turned into a bit of a monster."
Ms Burrows argued the department overstepped by sharing the diary, and asked for a list of the individuals, departments and agencies who had seen the contents.
"This brings back another issue for consideration as to whether the diaries were obtained ... for a collateral purpose," she said.
But NACC barrister Bora Kaplan SC said the government would not be obliged to give Lehrmann copies of his journal if it contained classified information.
"There is some information in the blue diary that has been marked that way," he said.
He contended Lehrmann had not identified any legitimate forensic purpose for seeking his diaries, which could undermine his subpoena.
The NACC's lawyers have one week to decide whether to apply to withhold the diary's contents because of classified information, or make a bid to set aside parts of the subpoena.
"The ball's in your client's court," Justice Brigitte Markovic told Mr Kaplan.
The case has been set down for a hearing on October 15.
The suit will land on the plate of the yet-to-be-named new NACC commissioner, after the incumbent Paul Brereton on Monday announced he was resigning from the position three years into his five-year term.
Lehrmann is accused of gathering the confidential information on the French submarines in March 2019, days after he allegedly raped his colleague Brittany Higgins in senator Linda Reynolds' office at Parliament House.
He has denied the sexual assault claims, which remain untested in a criminal court.
But Federal Court Justice Michael Lee found in 2024 the allegations he raped Ms Higgins were proven on the balance of probabilities.
That finding was upheld twice by the Full Federal Court and the High Court.
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
14°C