Police have declined to name those involved but authorities have confirmed the men were arrested in far north Queensland as they towed the dinghy from Melbourne towards Cape York.
It's an alleged plot involving a high-risk sea passage in a seven-metre tinnie.
Police allege the five men planned to take their boat to Indonesia and then fly on to Syria.
According to Attorney-General George Brandis, all five had cancelled passports.
"So the suspicion is that they were seeking to leave Australia to avoid the fact they couldn't travel by air because their passports had been cancelled. They are currently still in custody and police will make decisions in relation to whether or not charges will be laid."
Australian Federal Police Assistant Commissioner Neil Gaughan says the arrests relate to potential offences concerning incursions into foreign countries to engage in hostile activities.
"I must stress that the investigation remains active and is focused on ensuring community safety and disrupting criminal activity, either on Australian soil or by Australians attempting to join overseas conflicts. I would like to emphasise this is at the very early stages of the investigation and we have a significant amount of information to be assessed and analysed."
Named in media reports as among those arrested is Musa Cerantonio, who has supported calls for jihad in Syria and Iraq, and Shayden Thorne, who served four-and-half-years in jail in Saudi Arabia for possessing terrorism-related materials on his laptop.
He was granted clemency and deported to Australia in 2014.
George Brandis says eight search warrants were executed in Melbourne following the arrests.
"The arrest of these five men in Far North Queensland demonstrates once again the threat to Australians, or the threat of Australians engaging in acts of terrorism, including acts of terrorism in foreign countries, remains very real. There has been a high level of interagency cooperation."
While reassuring the public there is NO direct terrorism threat here as a result of the arrests, Deputy Victorian Commissioner Shane Patton says authorities nevertheless had to intervene.
"We have an obligation here in Victoria and Australia to make sure we don't allow these people to exit Australia. We know there would be people saying 'why don't you simply just let them go and take their chances in the waves and fighting in Syria?' We can't do that, we can't allow Australians to leave Australia and support terrorism anywhere. Additionally if we allow these people to fight in Syria and if they come back, they are combat-hardened."
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