Police have raided properties in Melbourne's north and west linked to five men charged over an alleged plan to travel by boat to Indonesia in a bid to join Islamic State.

The Melbourne men were arrested last week north of Cairns, but properties linked to the group were raided on Tuesday morning.

"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 police spokeswoman said.

"This operational activity is not linked to any increased threat or danger to the community. As the matter is before the court, we are unable to comment further."