In an open letter to Hellenic Football Federation (EPO) president Sofoklis Pilavios, general secretary for sports Panagiotis Bitsaxis criticised the Super League's credibility to run the country's top flight.
A players' strike was averted on Thursday after the players' union (PSAP) failed to get the backing of all 16 top flight clubs amid growing discontentment with violence inside and outside Greek stadiums.
"The Super League, under the circumstances it currently operates, is unfit to organise a championship. EPO must provide a clear plan with which to deal effectively with organizational and disciplinary issues and the subjects of violence and safety," said Bitsaxis.
"The organization of football based on the principle of self-governance must get its house in order to ensure the reliability, soundness and compliance with legality, without regulatory actions from the Greek state.
"The Government has repeatedly stated that it respects the autonomous state of football, but also makes it unequivocally clear that self-governance ends where the public interest begins."
Violence inside and outside stadiums has been a constant problem for authorities this season.
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