A Hellenic Football Federation (EPO) appeals committee upheld an earlier decision not to give Iraklis a licence for next season's Super League as they failed to fulfil UEFA's criteria which states teams should not have unpaid debts.
However, Athens club Panionios will play in the Super League next season after winning their appeal against demotion.
Panionios and Iraklis finished the season on 35 points, four clear of the relegation zone, but both clubs have been dogged by financial problems.
It is still unclear which team will take Iraklis's place in the top flight next season.
According to EPO rules, a team from the second tier should be promoted. But the Super League has appealed to EPO's judicial court stating that Asteras Tripolis, who were relegated after finishing third from bottom, should remain in the top division.
An EPO spokesman said the Super League's appeal will be heard next week.
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