Fundamentalist Christians charged over their alleged harassment of Muslims at mosques around Brisbane will fight the charges, their leader says.

Pillar Baptist Church pastor Logan Robertson was deported after being arrested in Brisbane earlier this month, but made the comments in a video he posted online.

Three other men also arrested after incidents at mosques at Darra and Kuraby, south of Brisbane, are were charged with public nuisance, trespass and entering a premises with intent to commit an offence.

"They're obviously going to plead not guilty because they're not guilty of the charges," Mr Robertson said in a video posted online.

The group did not appear in the Holland Park Magistrates Court in Brisbane today, but was instead represented by a lawyer.

It is unclear how Mr Robertson's own case will proceed, after he chose not to fight a deportation order issued by the Department of Home Affairs.

It is believed he is currently in the Philippines.

Police confiscated cameras from religious fundamentalist Logan Robertson. ( ABC News )

The case was adjourned until September 20, giving police time to provide a brief of evidence to the defence.

A warrant was also issued for Mr Robertson. However the warrant was postponed until the next court date, when formal details of his deportation were expected to be provided to the court.

The Pillar Baptist Church, which has a small congregation in Brisbane and has a history of opposing Islam, abortion and homosexuality, is not affiliated with the Queensland Baptists or the Australian Baptist Ministries.

Police seized recording equipment and charged the four church members after they travelled together to an Islamic school and two mosques and allegedly verbally abused worshippers.

The Pillar Baptist group was stopped by police a short time later, Mr Robertson was taken into immigration detention and had his visa cancelled.

Home Affairs Minister Peter Dutton said Mr Robertson had already been counselled prior to arriving in Australia last year about his past behaviour.

Mr Robertson was filmed as he confronted worshippers outside a mosque at Kuraby. ( ABC News )

In a video posted online on July 21, Mr Robertson said he chose not to appeal against his deportation after spending 12 days in immigration detention.

"The lawyer said if I want to get my visa back it's going to take at least three months of waiting in that detention centre and costs about 10 grand," he said.

"I've got better things to do so I just decided to go voluntarily.

"Just saying you hate the religion now gets you deported from a country. How sick is a government that would do something like that?"