Hi Jim,
The short, detailed, correct and possibly unhelpful answer is that you'll need to follow the CASA Regulations 1998, Subpart 101.E, concerning unmanned free balloons.
https://www.comlaw.gov.au/Details/F2015C00997/Html/Volume_3#_Toc438545387If your payload is under 50 grams then you're in the "light balloon" category without approval needed.
Otherwise, above that, you're in the domain where you will need CASA approval and ATC clearance, they will issue a NOTAM etc.
So if you can engineer your payload hardware to <50 grams then it's well worth it.
If in doubt in terms of interpreting the legislation then I suppose the best action is to ring up CASA, and have some idea of your launch location, date, time, balloon size and payload mass.
I would just explain that it's basically just a weather balloon for scientific/educational purposes operating within a typical altitude for a meteorological balloon. Don't call it a spacecraft because (a) it's not close to space and (b) because I think it will be easier for the CASA person to understand what you're on about.
These links may be helpful and interesting too.
http://www.informationtechnologies.com.au/files/HAB%20Presentation.pdfhttp://wotzup.com/2013/09/australians-applying-to-casa-for-a-hab-flight/http://wotzup.com/2014/03/pico-balloon/Hope this is helpful.
Cheers,
Luke