It's been a while since I researched it; however, charges at military bases used to work like this:
- Military do not charge any sort of enroute/ATS fee. I'm pretty sure that, under the Defence ACT, Defence is not permitted to charge for any 'service' it provides.
- Military owns and maintains all the infrastructure at its bases (Darwin, Townsville and Willy included) including RWYs, TWYs, NAVAIDs, lighting, RADARs etc.
- Military does not charge landing fees at its bases (as per above).
- Where there is a civil terminal at a military base (ie Darwin, Townsville and Willy) the local airport corporation collects a landing fee.
- In return for use of its infrastructure, military aircraft do not pay enroute fees to AsA, or landing fees at its own bases.
Like I said, this may have changed but not to my knowledge.