A group of men arrested while allegedly trying to join an Islamic State faction by boat were first reported to police by a jogger who heard them chanting passages from the Qur’an and saw them carrying an Isis flag near Melbourne’s Flemington racecourse, a court has heard.

Robert “Musa” Cerantonio, Paul Dacre, Shayden Thorne, Kadir Kaya, Murat Kaya and Antonio Granata are fighting allegations they planned to sail from Cape York to the Philippines to join Isis sympathisers last year.

The men appeared before Melbourne magistrates court on Monday for a committal hearing that will determine whether they should stand trial. All six have been charged with making preparations for incursions into foreign countries to engage in hostile activities.

The first witness to give evidence at the hearing said he had seen a large group of Muslim men at the back of Flemington racecourse in Footscray while he was jogging in July 2015.

Yonatan Hewet, who speaks Arabic, told police the men were chanting part of the Qur’an, the court heard. He also saw they had a black Isis flag with them.

Several months after Hewet reported what he saw to police, Cerantonio, Dacre, Thorne and Kadir Kaya were arrested near Cairns towing a seven-metre boat en route to Cape York.

Murat Kaya was arrested in Victoria during counter-terrorism raids days after his co-accused were arrested in far north Queensland. He is accused of helping the others buy a boat that they were allegedly planning to use to reach a growing Isis faction in the Philippines.

More than 20 lawyers are at the bar table at the men’s committal hearing, representing defence and federal prosecutors.

Before the hearing started, several federal agents were asked to leave the courtroom after counsel for Cerantonio, Michael Cahill SC, said he was concerned there was an “issue of collusion” between Australian federal police investigators against his client.

He said AFP agents had emailed discussing going through their statements together. “It clearly raises the issue of collusion,” he told the magistrate, Charlie Rozencwajg. “We seek the informants out of court … to put the brakes on that.”

The committal hearing continues.