The home affairs department has warned the auditor general it may try to suppress his findings if he presses ahead with a planned report on its $330m fleet of patrol boats.

The warning comes just months after the Coalition took the unprecedented step of suppressing a separate audit critical of a $1.3bn arms deal with the multinational arms manufacturer, Thales.

It has prompted renewed fears that the Thales case will prompt a flurry of attempts to suppress criticism from the auditor general.

The auditor general, Grant Hehir, is currently scrutinising the in-service support arrangements of the Cape Class patrol boats, which are used by home affairs to monitor Australia’s coastline for illegal activity.

His report is due to be tabled next month, but internal correspondence reveals that the home affairs department has flagged it will try and suppress some of his work.

Mark Brown, a home affairs department first assistant secretary, wrote to the auditor general last month, warning that the department may seek to have the attorney general, Christian Porter, redact parts of the report.

It would be only the second time those powers have ever been used. They were used for the first time in June.

Brown raised “potential prejudice to the commonwealth’s commercial interests should that material be published”. He also warned the publication risked threatening Australia’s national security.

“Also as discussed at our meeting on 2 October 2018, we are concerned about potential prejudice to national security should identified parts of the material contained in the report be published,” he said.

The correspondence has been tendered to a Senate inquiry examining Porter’s suppression of the Thales report. That report was highly critical of the cost effectiveness of Australia’s purchase of a new fleet of combat vehicles, the Hawkei, which infuriated their manufacturer Thales. Thales subsequently asked Porter to suppress parts of the report that effectively suggested Australia could have paid half the amount if it had purchased vehicles through a United States program, named the joint light tactical vehicle (JLTV).

The correspondence also reveals that the organised and serious crime agency, the Australian Criminal Intelligence Commission (ACIC), has flagged a potential application to suppress an auditor general’s report. The ACIC said it was considering taking the step if necessary to protect its data.

“I reiterate, 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’s chief operating officer, Paul Williams, wrote to the auditor.

The auditor general has previously revealed that two other agencies had flagged potential suppressions of his work since the Thales case.

Hehir expressed concern at the developments and warned the Thales case may have set a precedent.

But he had previously refused to name the new agencies seeking the suppressions, saying he wanted to protect his relationship with government departments.

Hehir has now changed his stance, revealing the names of the agencies in responses to questions on notice to the Senate inquiry.

The deputy chair of the inquiry, Labor MP Julian Hill, said the new attempts to suppress the auditor backs up concerns that the Thales case had a chilling effect.

“Confirmation that the already secretive department of home affairs has cottoned on to the attorney general’s unprecedented gagging of the auditor general, backs up concerns about the chilling effect on the auditor general’s independence,” Hill said. “The media, the public, and the parliament should all be concerned if agencies start threatening section 37 [suppression] applications to avoid or reduce public scrutiny,” he said.

A spokesman for Porter said he is yet to receive any new applications for suppressions.

“There are no further s37 matters presently before the attorney general and should any arise in the future they would be dealt with carefully and thoroughly on their merits,” he said.

Home affairs and the ACIC have been approached for comment.