I'm glad that you have found the book helpful.
The paragraph you mention comes from an EOT statement - i.e. if you rent a house for less than 3 months to one party then it is classed as a holiday rental and you are required to obtain an EOT licence.
For a long term rental a copy of the signed contract between the two parties (owner and tenant) should officially be registered at the tax office by the owner, and such contracts usually run for 1 to 3 years. A three month contract term may not actually be recognised by the tax office (I can't confirm this) as in Greek law (current @ 2006) tenants and owners both have rights for 3 years in a rental contract. Which means that in effect many contracts would not actually stand up in court if it came to it.
The tax office will be able to tell you if a 3 month contract is accepted by them , and if it is then I guess that is your proof? I don't understand to whom you are trying to 'prove' the long term rent .. to EOT?
As I say in my book "Individuals should always consult the relevant authorities, a Greek lawyer or accountant about legal and taxation issues relating to their personal circumstances."
Please remember that this info is for guidance, it is not professional advice.