The anti-corruption watchdog has sensationally claimed that Bruce Lehrmann's blue Moleskine diary contains some of the 'most sensitive material ever held by the Australian government', court filings say.

The bizarre claim was revealed in documents lodged in the Federal Court this week amid Lehrmann's civil case against Special Minister of State Don Farrell and the outgoing National Anti-Corruption Commissioner Paul Brereton.

Officials from the National Anti-Corruption Commission (NACC) raided Lehrmann's home in Tasmania in June 2024 as part of an investigation into claims that he misappropriated secret documents related to French submarines.

They were searching for sensitive documents about the now-abandoned submarine project Lehrmann was accused of stealing in 2019 from his ex-boss, former defence industry minister Linda Reynolds.

Lehrmann denies the allegation and is suing Commissioner Brereton and federal Labor government minister Farrell over legal costs he incurred during the investigation.

Federal Court Justice Michael Lee in April 2024 dismissed claims that Lehrmann had been involved with the submarine contracts - but that didn't stop the NACC from pursuing the investigation two months later and holding on to his personal diary.

Submissions lodged in court and seen by the Daily Mail show Lehrmann wants his diary back, and is dumbfounded as to how his handwritten scrawls could possibly amount to a security issue.

In his submissions, Lehrmann also asked why the contents of his diary - marked as 'protected' and 'secret' by the NACC - had been shared with the departments of Home Affairs and Defence, even though no allegations have been made against him.

The exact content of the diary is unclear, but Lehrmann said in his affidavit that it contains handwritten notes from 'ordinary daily meetings during the years 2018 and 2019'.

He said the meetings included senior cabinet ministers, prime ministers, lawyers and political staff during his time as a senior policy and national security adviser.

The blue diary seized by NACC was also one of five he kept over his eight years in politics. Four diaries remain in his possession.

In the submissions, Lehrmann said 'a personal diary is among the most intimate personal documents a person possesses. It records private thoughts and observations never intended for any government agency.'

Lehrmann also said the NACC's suggestion that the diary contained material of 'national security sensitivity' was inconsistent with the Commissioner's 'complete silence on the issue' for almost two years.

'If the material was genuinely that sensitive, it is inconceivable that no steps were taken during that period to formalise any claim, or to notify [Lehrmann],' the submissions read.

The NACC also refused to take part in a court undertaking to ensure the contents would not be distributed any further, according to court documents.

In court on Wednesday, Lehrmann's lawyer Zali Burrows told the court that her client was not told when the NACC distributed the diary to other ministerial departments. 

Ms Burrows argued that 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 said that Lehrmann had not identified any legitimate forensic purpose for seeking his own diaries.

The NACC's lawyers have a week to decide whether to apply to withhold the diary's contents because of classified information, or make a bid to set parts aside.

Lehrmann has asked the NACC to surrender the diary into the custody of the Federal Court. 

Claims about the French submarine contracts were first advanced during Lehrmann's rape trial in the ACT Supreme Court in 2022. 

Lehrmann told the court that he did not rape his colleague Brittany Higgins in their former boss Reynolds' Parliament House office in March 2019. 

It is agreed that they both went back to Parliament House together in the early hours of the morning, but their stories depart from there.

Higgins said he raped her. Lehrmann said he made notes on Question Time briefs about French submarine contracts and went home. The criminal case was eventually abandoned due to misconduct by a juror.

The contracts came up again during Lehrmann's defamation trial against Network Ten and Lisa Wilkinson in 2023, when Lehrmann told the Federal Court he worked on Question Time briefs rather than raping Higgins.

However, Justice Lee found that, on the balance of probabilities, Lehrmann did rape Higgins and dismissed the French submarine argument.

'Commonsense suggests that it is obvious there was one dominant thought running through the mind of Mr Lehrmann as he was approaching Parliament House, and it was nothing to do with French submarine contracts,' Justice Lee said.

That finding was upheld by the Full Federal Court and then by the High Court.

Lehrmann has always denied raping Higgins.

The case against the NACC has been set down for a hearing on October 15.

The matter will be handled by the new NACC commissioner after Mr Brereton on Monday announced he was resigning from the position three years into his five-year term.