One offs are different?
Disregarding the validity of the patents, which has been well commented on already, I thought that patent protection only applied to people or organisations who were producing an infringing item/system for general sale.
e.g. If I had the ability and resources, I could produce an exact copy of an iPad and use it for my personal use with no legal redress from Apple. (I'm not considering the trademark aspects here, just the patents, though my reasoning also applies too the trademark.) As long as it's for my personal use and I don't try to sell it.
Similarly, I can ask someone else to produce an exact copy of an iPad for my personal use and that would also be ok, provided that I had specifically asked them to do that and that did not make a habit of doing this for lots of people.
If the Australian government (or any individual) specifically asks for one specific computer system to be built to its own requirements, in terms of characteristics and methods, then it doesn't matter if any patents cover that system because it is not being built/sold for general sale.
IANAL so can a legal beagle please comment?