Influential preacher Musa Cerantonio, as well as Shayden Thorne, Paul Dacre, Antonio Granata and Kadir Kaya, were flown from Cairns on Thursday after they were arrested last week.

Police allege the men towed a boat from Victoria to far North Queensland with the intention of sailing to Indonesia, before heading on to Syria.

There was an increased security presence in a packed Melbourne Magistrates Court when the men appeared, with protective services officers spread around the perimeter of the public gallery

More than 20 friends and family were present, including Shayden Thorne's brother, the notorious, self-styled, firebrand preacher Junaid Thorne.

Juanid Thorne was among a handful of supporters of the men who refused to stand for Magistrate Luisa Bazzani when she came into the courtroom before the hearing began.

"It is customary ... for people to stand," Ms Bazzani said.

"There appear to be some who would prefer not to stand ... it denotes to me a lack of respect.

"That lack of respect to the court may be relevant at another time."

The five men's lawyer, Robert Stary, told Ms Bazzani that his clients' supporters' religious convictions prevented them from standing.

"They stand for no one other than Allah, that's the basics of it your honour," Mr Stary said.

He pointed to the case of Abdul Nacer Benbrika, convicted of terrorism offences, where Justice Bernard Bongiorno allowed people not to stand.

"I don't share that position," Ms Bazzani said.

"I consider it absolutely disrespectful."

Each of the men were charged on May 15 with making preparations for incursion into foreign countries - Isis-controlled Syria and northern Iraq - for the purpose of engaging in hostile activities.

The men face a maximum penalty of life in jail if found guilty.

They were placed in the dock behind glass, due to the "sheer number" of them, Ms Bazzani said.

It was the first time in custody for Mr Cerantonio, 31, Mr Dacre, 30, Mr Granata, 25, and Mr Kaya, 21.

It was the first time Mr Thorne, 27, who the court noted was an Indigenous Australian, had been in custody in Australia.

The only medical issues arising from the hearing were obtaining Mr Granata's anxiety medication and glasses for Mr Thorne.

The five accused remained quiet throughout the brief hearing, with some waving at supporters as they were returned to the cells.

The group were remanded to appear in court again on September 22.

Outside court, Mr Stary asked why the accused were allowed to reach Cairns given police allege their suspicious behaviour started in Melbourne.

The lawyer drew a comparison with the Bali Nine case, where Australian drug smugglers were arrested in Indonesia rather than Australia, even though authorities had suspicions about them at home.

"This is not about having trophies in a cabinet, about having successful convictions, this is about making Australia a safer place," Mr Stary said.

"In a different context we saw what happened with the Bali Nine — now we see it again."

"I direct any further questions to Mr Brandis [Attorney General George Brandis], he seems to make all the pre-election commentary in this case," Mr Stary said.

With AAP