Have to agee with John in regards to the legal system! The legal system in Oz is seriously broken, unless you can afford the biggest and best QC you are stuck in the system.
You start off with the Magistrates Court or Federal Magistrates Court and unless you plead guilty straight up you get stuck going through mentions, committal hearings etc for at least a year.
Then it starts all over again with mentions in the district court (or in John's case the AAT)...etc..etc until you get a court date. As a consequence the simplest cases (on paper) can drag on for years, so even if your innocent you become tempted to plead guilty just to have it over with.
Not to mention the huge financial burden you have been put under to prove your innocence! Like I said the "legal system is broken"!
That said I have to agree with Wallsofchina in regard to:
However the Federal Ombudsman may have the power to investigate what could be an abuse of process by Department of Transport and Regional Services.
....although I think you would be better going straight at CASA, being a government authority (i.e. CASA fall within the realms of the Commonwealth Ombudsman). A good brief could highlight the double standards of the regulator and the inconsistencies of their argument, which has been pointed out in the various posts in this thread.