Olympiakos Volou and Kavala were handed a Super League reprieve on Wednesday after a decision by the Hellenic Football Federation to overturn the Super League's decision to demote them to the second division, but the Volos club is expelled from the Europa League.
The federation's appeals committee decided instead to punish the two clubs for their roles in a match-fixing scandal by deducting points before the start of the season later this month.
Volos will start the season with minus 10 points and Kavala with minus 8 points.
Last month the disciplinary of the Super League had voted to relegate both clubs to the second divisio
However both teams appealed that decision with the federation leading to Wednesday's reprieve for thclubs.
The decision to take off points for Volos means an automatic expulsion for the club from the Europa League play-offs by the European football governing body UEFA. They were due to face French giants Paris Saint-Germain next week.
"The cleansing process has got its ups and downs," commented a worried Sofoklis Pilavios, the head of the Hellenic Football Federation.
"I am concerned by the decision but I have not yet read the thinking behind it," he added.
The federation decided to keep the punishment for the two club owners, Achilleas Beos (Olympiakos Volou) and Makis Psomiadis (Kavala), who were fined 90,000 euros each and banned for life from any involvement in football.
Beos, who has since handed over ownership of Volos to a consortium, was arrested in June and accused of being at the centre of a ring that fixed matches so members could make money from betting on the games.
Psomiadis remains at large, although his son, Stavros, who is officially Kavala's president, was arrested and released on bail.
With Olympiakos Volou and Kavala remaining in the Super League, Larissa and Panserraikos who were to replace them, will stay in the Football League.
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