Counter-terrorism police on Tuesday carried out raids across Melbourne connected with five men accused of planning to travel to Syria to join Islamic State via a journey that would start with a motor boat trip from Australia to Indonesia.

"The Victorian Joint Counter Terrorism Team are currently executing a number of warrants in the northern and north-western suburbs of Melbourne as a part of Operation Middleham," a Victoria state police spokeswoman said.

The men, aged between 21 and 31, were charged on Saturday with preparing to enter a foreign country "for the purpose of engaging in hostile activities," an offence that carries a maximum penalty of life imprisonment.

The five, who were not named, were arrested last week after towing a seven-metre (23-foot) motor boat almost 3,000 km (1,865 miles) from Melbourne to Cairns in northern Queensland state.