I guess its really a state by state thing as the maritime authorities are state based organisations. Waterways in NSW does not seem to be as enlightened as the Vic one - did some more looking and the current NSW boating handbook on the Waterways website has under its special areas page :
Seaplanes
Seaplanes when on the water are just like
any other vessel. They are subject to all the
restrictions and privileges of other boats and
conduct their operations accordingly. Like other
boat operators, seaplane pilots hold marine
boating licences to operate a vessel at speeds in
excess of 10 knots. Don’t be alarmed if a small
seaplane alights or takes off in the waterways
near you. Seaplane pilots are specially trained
and qualified to operate upon the water. If
you’re running straight, don’t suddenly change
course to avoid the seaplane.