The abuse against Cisse, the leading scorer in the Super League, allegedly came after last weekend's derby at Karaiskakis Stadium when league-leading home team Olympiakos beat second-place Panathinaikos 2-1 and increased their lead to 10 points.
A number of fans rushed the pitch after the match and some abused and attacked Panathinaikos players, including Cisse, television video showed.
According to the lawsuit filed at the Athens first instance court prosecutor's office, Cisse said that for the first time in his career he felt the threat of being seriously injured.
Cisse asked that Marinakis be punished for his actions with whatever the law allows and that he would also file a protest to European football's governing body UEFA.
He said he never provoked the actions from the fans nor the "ironic and abusive behaviour" from Marinakis who is also president of the Super League.
"Football is a sport and not a war," Cisse said in the lawsuit.
Cisse also accussed the Olympiakos fans of racist behaviour throughout the match.
"These kinds of actions offend out culture," Vervesos said on behalf of his client.
"It is a pity to see such behaviour from people who have to rethink their attitudes and behaviour. We will go everywhere, UEFA, FIFA, to find justice. We are very upset with what is happening and we are deeply disappointed."
After Friday's practice session, Cisse again told reporters that he will leave Panathinaikos after this season.
"I was very disappointed after the match and said under these circumstances I would leave. There are still seven matches remaining and we must do our best, but nothing has changed to what I said about whether to stay or leave," he said.
The Greek government on Monday condemned the violence at the derby and authorities have pledged to take action to stop such incidents in the future.
The Piraeus prosecutor's office has requested copies of the videos in order to investigate and press charges against the hooligans.