A magistrate has refused bail for two men arrested following yesterday's terror raids after considering submissions overnight.

Reg Marron today remanded suspects Hany Taha, 31, of Hadfield and Abdulla Merhi, 20, of Fawkner, to reappear in Melbourne Magistrates' Court on January 31. They are charged with being members of a terrorist organisation

In refusing bail for the pair, Mr Marron said evidence of the group's discussions of its intentions to carry out a jihad in Australia and its belief it was justified in killing innocent people was alarming.

"Notwithstanding their (the applicants') personal circumstances and personal history, it is extremely alarming,'' Mr Marron said.

The magistrate said the prosecution's case could be described as a ``work in progress'' and there was little evidence to link the Melbourne group to a group arrested in raids in Sydney yesterday.

"(But) . . . weighing up all the evidence, I'm not satisfied that either applicant has demonstrated exceptional circumstances. I believe the application is premature."

Mr Marron said that although police did not know the name of the organisation to which the two suspects allegedly belonged — or their relationship with each other — there were very serious issues raised by the prosecution, namely that members of the group were found in possession of loaded firearms.

It had been said under oath that each of the applicants, particularly Merhi, were involved in discussions about martyrdom.

He said the court had also heard that both men were involved in discussions about firearms.

"After weighing up all the evidence, I'm not satisfied the applicants have shown exceptional circumstances," Mr Marron said.

He urged the media to be diligent in its reporting of the case. The matter had attracted unprecedented media reporting and there was a great risk the two men would have their chances of a fair trial jeopardised, he said.

"These men remain innocent until the prosecution establishes their guilt beyond reasonable doubt."

The deputy director of Corrections Victoria provided the court with details about the custody of the applicants while on remand following a query from Rob Stary, defence lawyer for Merhi, about whether they would be held in solitary confinement.

Paul Delphine said the two men would be held in the maximum-security Acacia wing of Barwon Prison, near Geelong.

He said he could not answer Mr Stary's question because solitary confinement was not part of corrections legislation.

Mr Delphine said the men would be housed in separate cells with a shower, toilet, electric jug, reading material and a television.

He said they would not have involvement with anyone until their situation was reviewed. They would be allowed three hours' exercise a day, which would increase to six hours every second day.

Arrangements would be made to meet the pair's religious needs, including specially prepared food and access to a spiritual leader.

They would be allowed one family visit a week. Corrections Victoria would consider increasing the access allowed to children. 

At the moment children are allowed one access visit a month. Taha has three children — aged six, five and one.

Mr Delphine said the men would not be restrained or shackled while on remand.

They were the only two of nine men arrested in Melbourne's anti-terror raids yesterday to apply for bail.

Taha's lawyer, Brian Walters, SC, told the court allegations against his client were vague and the case against him was not strong.

He said Taha had no prior convictions, was a married father of three young children and worked as a spray painter.

Merhi's lawyer, Mr Stary, said his client also had no criminal history, was recently married and his wife was expecting their first child soon.

Mr Stary said his client would vigorously contest the charges and if he was placed in custody, he would be remanded in oppressive solitary confinement.

Outside court, Mr Stary criticised politicians and the police chief commissioners of NSW and Victoria who yesterday commented on the case.

"Regrettably, as a result of yesterday's performance particularly by senior politicians and various chief commissioners and other people, the presumption of innocence has effectively been removed against these men,'' Mr Stary said.

He urged the community and media to respect that the matter was before the courts.

"We don't want it to be some quaint notion that a person is presumed innocent, we actually want that to come into practice and we would ask that the community and media would respect that notion.''

The remaining seven yesterday made no bail application and were remanded in custody until January 31.

Among the seven was Muslim preacher Abdul Nacer Benbrika (also known as Abu Bakr), 45, of Dallas, who was charged with directing the activities of a terrorist organisation and being a member of a terrorist organisation.

Ezzit Raad, 23, of Preston; Aimen Joud, 21, of Hoppers Crossing; Fadal Sayadi, 25, of Coburg; Ammer Haddara, 26, of Yarraville; Ahmed Raad, 22, of Fawkner and Shane Kent, 28, of Meadow Heights were charged with being members of a terrorist organisation. 

- theage.com.au with AAP