The report, to be released on Wednesday, will also reveal last year's cyber-attack on the Bureau of Meteorology was the work of a foreign power, which managed to install malicious software and steal sensitive documents.
Dan Tehan, the minister assisting the prime minister for cyber security, wouldn't specify which country, but said it showed cyber espionage was alive and well.
"We have to make sure that we're taking all the steps necessary to keep us safe, because the threat is there and the threat is real," he told ABC radio.
Peter Jennings from the Australian Strategic Policy Institute believes the Bureau of Meteorology was targeted because weather prediction is big business for countries looking to maximise crop yields, and deciding when to harvest.
He says the bureau is also linked to other government departments, including defence.
The Australian Cyber Security Centre says a recent series of brazen attacks on high-profile entities shows there's a willingness to use disruptive and destructive measures to seriously impeded or embarrass organisations and governments.
Local government networks suffered 1095 serious cyber assaults in the 18 months to June 30 this year, The Australian reported on Wednesday.
Special advisor to the PM Alastair MacGibbon says the information gained would potentially be valuable to another country.
"It looks at earthquakes, it looks at a whole range of things vital to our economy, doesn't surprise me that a foreign nation would be interested in that type of information" he added.
But the 2016 Threat Report warns this can rise and estimates that within three years terrorists will be able to compromise networks with destructive effect.
Mr Tehan said the threat of a cyber-attack from terrorists is currently ranked low but acknowledged Australia's digital integrity was being increasingly tested.
"We are ahead of the terrorists now and that is where we must remain," he wrote in The Australian.
