Seed Savers Connect

Unless you want to start a National organisation, registering a incorporated association is done at the State or Territory level. 

Information on the processes for incorporated associations for each state are here:

NSW – … operatives
QLD – … or-profits
SA –
Tas – … sociations
ACT – … -questions
NT – … sociations
Vic – … sociations
WA – … -and-clubs

The rules for each state are similar but the laws, processes, and fees are different in each state.