The Greek federation (SEGAS) have announced the two - who were Olympic medal-winning sprinters four years ago - will face a disciplinary hearing early in the new year.
Kenteris - 200metres gold medallist in Sydney where Thanou was runner-up in the 100m - has, like his compatriot, denied all charges levelled at him of deliberately missing three out-of-competition drug tests.
But the International Association of Athletics Federations (IAAF) announced last week there is a case to answer and provisionally suspended the pair and their coach Christos Tzekos.
Tzekos faces allegations that he distributed and assisted in the use of prohibited substances and tampering with the doping control process.
SEGAS will set up an independent tribunal in January, designed to “find out the truth and reach a just decision.”
The athletes’ lawyers Michalis Dimitrakopoulos remains confident his clients - who have denied all of the allegations - will be cleared.
Kenteris and Thanou also face civil charges they faked a traffic accident in Athens on August 12, using the incident as an excuse for not turning up for a drugs test.
Subsequently both Greek stars withdrew from the Games where they were among the host nation’s major medal hopes.
If Kenteris and Thanou are found guilty of the charges they are likely to receive a two-year suspension - the agreed tariff set by the IAAF and World Anti-Doping Agency (WADA).