Marinakis, a shipping and media tycoon who also owns English Premier League club Nottingham Forest, and the four board members have denied any wrongdoing, including an accusation of supporting a criminal organisation linked to Olympiacos fans.
"The accusation is totally baseless," Marinakis' lawyer Vassilis Dimakopoulos told Reuters. A trial date has yet to be set.
Authorities launched the probe after a riot police officer was fatally injured by a flare in clashes with a group of Olympiakos fans outside a volleyball game in December 2023. A separate trial is underway for the killing.
The volleyball match was between Olympiacos and Panathinaikos.
The judicial council also decided that more than 140 people, most of them fans of the Olympiacos sports club arrested since April, will stand trial on charges of participation in an alleged criminal organisation. The council decision follows a magistrate's investigation.
Lawyers representing them say they have denied the accusations, as has Olympiacos football club.
Sport in Greece has been marred by violent incidents on and off the pitch in recent years, and authorities have repeatedly promised to eliminate hooliganism.
Marinakis has accused the conservative government of interfering with the media and justice to protect its image. In a statement on Olympiacos' website on Thursday, he said the real target was press freedom, democracy and his own media group.
"It is a coordinated, but desperate, effort to silence me," he said.
A government spokesman responded that citizens were equal before justice, which is independent.