A court hearing for six men accused of a plot to sail a small boat to Indonesia to join Islamic State has heard that as many as 50 men and women were seen in a Melbourne park waving the terrorist organisation's flags and chanting anti-Western slogans.

Musa Cerantonio, Paul Dacre, Kadir Kaya, Murat Kaya, Shayden Thorne and Antonio Granata were arrested last May and charged with terror-related offences over the alleged plot.

The witness says he saw flags such as this being waved in a Melbourne park. Credit:Michael Bachelard

The six men appeared in the Melbourne Magistrates Court on Monday for a preliminary hearing.

Businessman Yonatan Hewet, told the court he was running at Footscray Park when he saw a group of men and women chanting religious verses from the Koran in Lebanese-accented Arabic in July 2015.