Islamic preacher Musa Cerantonio, Shayden Thorne, Kadir Kaya and two others were charged with preparing to enter a foreign country on Tuesday to engage in hostile activities.
They face a maximum penalty of life in prison if found guilty.
The men, aged between 21 and 33 years old, were arrested after they allegedly towed a 7-metre fishing boat from Melbourne towards Cape York.
The group are due to face a Cairns court on Monday where prosecutors are expected to apply for their extradition to Melbourne.
Police would not disclose how long ago the men travelled from Melbourne to northern Australia but believed they were intending to travel through Indonesia and the Philippines to Syria.
AFP Deputy Commissioner Neil Gaughan on Tuesday said the men were "very committed" to leave the country after previously having their passports cancelled.
"The fact that they'd gone all the way from Melbourne, all the way to far north Queensland, indicates that these people were extremely committed in ... their attempt to leave the country," he said.
AFP allege the men purchased the boat in Melbourne before travelling to Queensland.
Police said they had been investigating the men "for weeks" and there was no domestic terrorism threat arising from the investigation.
In a statement, the AFP said there was "no current or impending threat of a terrorist act to the Australian community arising from this investigation".