The arrests by counter-terror police follow a series pre-dawn raids across Sydney and Brisbane in September as concern mounts about the flow of people to Iraq and Syria to fight with the Islamic State group and other jihadists.
More than 70 Australians are currently fighting for Islamic militants overseas. At least 20 have died and there are fears that increasing numbers of youths are being radicalised and could mount attacks at home.
One of the men charged late yesterday, a 20-year-old, was accused of being in "possession of documents designed to facilitate a terrorist attack" while a 21-year-old was accused of breaching a control order issued by a judge.
He said the targets were in Sydney, but did not go into detail.
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"I am confident that we've disrupted the activity that they were planning. And that is all I'm prepared to say at this particular point."
The arrests follow warnings yesterday by Prime Minister Tony Abbott of heightened "terrorist chatter" in the aftermath of a fatal cafe siege in Sydney's financial hub last week.
Iranian-born gunman Man Haron Monis, who had a history of extremism and violence, took 17 hostages in the city's financial heartland, unveiling an Islamic flag.
"A briefing from the security agencies today indicated that there has been a heightened level of terrorist chatter in the aftermath of the Martin Place siege," Abbott said yesterday.
"That's why it's important that people remain alert and aware as well as reassured that our police and security agencies are doing everything they humanly can to keep us safe."
Australia has not officially branded the Sydney siege as a terrorist attack and Abbott declined to speculate on any potential new threat.