Defence has formally apologised to three whistleblowers who revealed how incorrect and even fabricated data was regularly inserted into security vetting applications.
Defence Minister Stephen Smith said defence department secretary Duncan Lewis had written apology letters to the three on Wednesday.
Those letters were either delivered or in the post, he said.
Mr Smith said the recommendation to apologise to the three defence officials was in his view absolutely correct.
"And that's been done," he told ABC Television.
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The issue emerged last year when the three Defence Security Authority (DSA) workers from the vetting centre in Brisbane told the ABC they regularly faked information, such as addresses or previous workplaces, on security documents. Defence initially rejected these claims.
In a report tabled in parliament on Wednesday, Inspector-General of Intelligence and Security Dr Vivienne Thom confirmed that was exactly what happened.
The problems arose because security vetting forms required applicants to provide a very detailed account of their life, including full dates and details of education, previous employers and overseas travel.
Many applicants simply didn't know all this information and left fields blank.
However the electronic forms would not upload to the Australian Security Intelligence Organisation (ASIO) unless all field were filled.
So vetting centre employees resorted to what were termed "workarounds", inserting their own data, sometimes moving dates to fill gaps or fabricating addresses or employers.
Defence is now undertaking the arduous task of checking all the applications for incorrect data.
Mr Smith said he could give no guarantee that someone had not slipped through the vetting process.
"My own judgment is in the high or top security levels, there is a low risk," he said.
"But that is not a risk that we can either be complacent about or take for granted and we simply have to go through security assessment by security assessment individually to ensure that each and every one are eliminated."
Mr Smith said 3100 of 5300 applications had been checked with no change to the outcome.
"I hope that is the outcome for all of them. My own judgment is we are dealing here with a low risk but it is a low risk which, if it comes to pass, there are high and adverse and serious consequences," he said.
