The target was described as a "small Australian company with contracting links to national security projects".
Australian cyber security officials dubbed the mystery hacker "Alf", after a character on TV soap Home and Away.
"While presenting at a conference in Sydney, an ASD official (who works for the ACSC) disclosed information about the theft of data from an Australian company", the statement said.
But Defence Industry Minister Christopher Pyne insists the data obtained from an Adelaide defence contractor was only commercially sensitive and not "classified" military information.
Clarke told the conference that "the compromise was extensive and extreme".
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The firm was subcontracted four levels down from defence contracts and had only one IT person. Dan Tehan, the Minister Assisting the Prime Minister for Cyber Security, had on Tuesday highlighted the case as a significant breach, though he did not provide details.
The federal government admits it still doesn't know who managed to hack top secret technical information about new fighter jet and navy vessels more than a year ago.
Mr Tehan said it was unclear who launched the incursion, but the Government was not ruling out a foreign government.
The hack included information on the F-35 Joint Strike Fighter, C130 Hercules aircraft and the P-8 Poseidon surveillance aircraft.
The Poseidon is a spy plane which Australia has bought.
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According to Mitchell Clarke, an ASD incident response manager, the stolen documents for a Navy ship could let a viewer, "zoom in down to the captain's chair and see that it's, you know, one metre away from nav chair".
"It could have been a state actor, it could have been cyber criminals, and that's why it was taken so seriously". He said they used a hacking tool called China Chopper, which is reportedly widely used by Chinese hackers. He said the organisation only had one IT person and that person had only been in the job for a short while.
The investigation by Australian Signals Directorate (ASD) found the company had not changed its default passwords on its internet facing services.
The secret information was restricted under the International Traffic in Arms Regulations (ITAR), the USA system created to regulate the export of defence and military-related technologies, according to Mitchell Clarke, an incident response manager at the ASD who worked on the case.
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