Auditor-General Grant Hehir revealed the department, and the criminal intelligence commission, were the first two agencies to signal they could try having sections of his reports blacked out.

Mr Hehir's audits provide one of the few avenues for the public to monitor the government's projects, and often give the evidence needed for MPs to cross-examine departmental bungles and waste.

Attorney-General Christian Porter's decision to suppress parts of a critical inquiry into a $1.3 billion military deal with French defence company Thales in June raised alarm among parliamentarians that he had set a precedent to redact other audits.

After Mr Hehir revealed last month other agencies had begun following suit by flagging suppressions, Labor MPs asked him to name them and criticised what they described as a Coalition attempt to shut down scrutiny.

In response to a joint parliamentary committee's questions, the national auditor said Home Affairs - overseeing Australian Border Force - and the Australian Criminal Intelligence Commission had signalled they could try invoking a law letting the government block publication of information deemed against the public interest.

Before Mr Porter suppressed parts of the auditor's report into the government's deal with Thales finding Australia could have paid half the amount for its new combat vehicle fleet, the legislation allowing the redaction had not been used.

Home Affairs told the national audit office in October it would consider seeking to redact another report - due next month - into in-service support for its Cape Class vessels patrolling for illegal activity on Australia's coastline, saying its publication would risk national security and the government's commercial interests.

"We seek your consideration of these matters in terms of potential prejudice to national security should that material be published," a departmental official wrote in a letter.

The criminal intelligence commission is in the Australian National Audit Office's spotlight after it had to abandon a disastrous multimillion dollar attempt to introduce facial identification technology in a new database for use by Australia's law enforcement agencies.

The project went $40 million over budget before the commission cancelled it. In a letter to the auditor, an official in July said it would consider seeking parts of the audit report be redacted, although it is unclear whether he was referring to the inquiry into the biometric program.

"This is not a matter of obstructionism – it is just us exercising our responsibilities so far as the protection of our data is concerned," the commission official said.

Labor MP and deputy chair of the joint public accounts committee, Julian Hill, said the auditor-general's revelations had confirmed concerns Mr Porter's decision to suppress the Defence audit could create a precedent for agencies to avoid scrutiny.

"The already-secretive Department of Home Affairs is the first department to flag it may seek the certificate to gag the auditor-general," he said.

"The auditor-general is one of the few watchdogs with real teeth and independence to hold any government of the day to account, and threats to his independence have to be taken very seriously."

Comment was sought from Home Affairs and the crime commission.

Mr Porter's order to black out sections of the audit report into the government's purchase of Hawkei vehicles from Thales drew accusations he had used national security reasons to cloak a suppression that served the company's commercial interests.

Documents released to a parliamentary committee show Thales Australia protested three times against information about the company's supply of the vehicles being included in the audit, before taking its complaint to the Attorney-General.

In highly-redacted letters from Thales Australia and New Zealand chief executive Chris Jenkins to Mr Hehir on November 30, December 12 and December 13 last year, the company attempted to stymie the publication, even after changes had been made on its request.

"The release of the report in its current form will cause significant and unjustifiable commercial damage. It will unfairly prejudice the commercial interests not only of Thales Australia but also the many supporting partners, suppliers and contractors of the Hawkei program, many of which are Australian [small to medium enterprises]," Mr Jenkins wrote on November 30.

Mr Jenkins said in another letter on December 13 that his previous correspondence expressed concerns that the audit report would unfairly hurt the commercial interests of Thales Australia and the federal government.

The letter also referred to the section of legislation governing the auditor-general that said Mr Hehir must not include information that was unfairly prejudicial to commercial interests. Thales threatened taking further action if the auditor did not remove the parts of his report it had identified.

In a letter to the committee investigating the matter, Mr Jenkins said its attempt to stop the report's publication through the Federal Court, as well as its request to the Attorney-General to redact the audit, had been vindicated by Mr Porter's decision to order the suppression.