Granted, I've never set foot in Australia, nor outside of the USA for that matter. my advice: It probably doesn't matter where, but it sounds like your piece will include some piece of logic as to why the base was put where it gets put. That would make it up to your writing talents to make that seem logical to us. Some factors your characters are likely to consider:
Proximity to sources of goods, materials, and fuels needed to keep it running.
Proximity to human residences- This one is tricky, because on the one side they'll want lots of people to work there to keep the place running, but they also know that it will likely be a site bombed first, and too close means more lives lost. Perhaps the government would build special residences for the employees/ service men.
Since it sounds like your threat is extraterrestrial, you also may want to consider placing several bases around the globe. Perhaps, somehow, a floating base or an air-ship type base would be useful. I don't know how far ahead you are technologically.