As far as I know you can't use the online system for 50cc bikes but the process has changed from last year. Previously I think you had to go to a kiosk, the tax office and the police station, not necessarily in that order. This year I think you have to get an e-paravola, take that to the bank and pay and then take the receipt to the police station. I am not 100% sure but I am meeting someone tonight who has done it so I will ask and report back tomorrow.
I checked with my friend tonight. He went to the police station where he normally goes to renew his circulation tax first. They printed out two e-paravolo, one for €12 and one for €3. He took the e-paravolo to the nearest bank and paid the €15. He then took the e-paravolo, with receipts from the bank stapled to them, back to the police station. Job done.
Not bad. A night in a taverna and I can still type something that makes sense. I'll just go and mop up the blood running out of my ears from the musicians who thought they were playing at the Odeon on the Acropolis not inside a 100 sqm taverna.
For a 50cc motorbike/scooter this is the procedure I had to follow:-
Drive to police station in Haniá and get a paper slip "Αίτημα Χορήγησης Παράβολου". (This slip might be available elsewhere. I didn't ask.) It is in two halves: one for €3 (on which the policeman wrote "ΚΕΠ") and one for €12 making €15 in total.
Drive to motorbike shop in Gogoni street where I bought the m'bike. The salesman knew what to do. He accessed a 4-letter Greek tax web site, clicked on a link (big choice - I didn't see which). That led to another page with a very, very long drop-down list. It took him a full minute to select an option from this list, which opened a two-page form to complete.
He printed out the two completed form pages then repeated the whole process because, he said, "you need two copies".
I had to take the forms to the (my) bank and pay the money. It took a few minutes for the information to be punched into the computer.
Then, with receipts and other paperwork in hand, I went to Vamos police station for updating and stamping the "ΑΔΕΙΑ" green registration booklet.
I suspect that the policeman wrote KEP on one of the papers because he was suggesting that you take them to KEP. KEP would have printed out the e-Paravolo for you just as the chap at the motorbike shop did. If you know what you are doing you can print them yourself. I suspect that this is the web site the chap at the motorbike shop used. Click on the button and you get the form to fill in. I didn't put a link directly to the form because I have found that such links often only work on the PC that originally accessed the form. I think you need to select the 13th item in the first box, ignoring the word "Επιλέξτε" and the 10th item in the second box. Not sure about the third box. No idea how to get the e-Paravolo for the €3.