Well assuming that nothing has changed recently it has to be done through an agent. The ECAA do this so there is a local middle man to collect your navigational charges and comms charges. On the positive side though it takes about 15 minutes to get a permit, as the agents already have predesignated overflight permit numbers which they issue to their customers upon application. Landing permits are a little different though, but still relatively straight forward.
Cheers,
Buzzz