Wartime powers can mean anything. In WW2 the Federal Government used the emergency powers to snatch more control from the states because of the disjointed state of the nation. So if you think the current iteration lacks control, think about how much less power they had pre WW2. Federation could quite easily have been several separate countries within Australia rather than one nation. The larger states governed as independent nations effectively, with their own separate armed forces and governance pre 1901. Victoria had its own navy, ships were HMVS (His Majesties Victorian Ship), including a coastal battleship, infantry, artillery and mounted horse regiments etc. This is why Australian states wield the power they do.
You would have to have much higher death rates going on for any emergency powers to be enacted against the states in a pandemic. There would have to be proof of an undeniable threat to the public that would warrant it.