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The site will be in google.com.au, as both use the same index (data). What you may mean is that your site does not show up for searches in pages from Australia...
If that is the case, Google uses some algo to determine where to put a given site. Say, if the web site is hosted in Australia by IP address location. Or if it is registered by someone in Australia according to whois. Or if pages that link to it are from Australia.
So, if your site does not yet show up in "search only pages from Australia" then you may need links from true blue Australian pages.
SEOe you need to own the .com.au version of your website to rank in the pages from australia section..
This simply isn't true. You can rank just fine with a .com.
I don't believe that it is possible for a site to do just fine in .com and not be indexed at all in .com.au - simply because they are the same index with a few different filters applied.
Perhaps consider hosting your site in Australia - but sites that I run generally rank quite similarly in .com and .com.au.
Hope that helps,
P.S. Welcome to WebmasterWorld, SEOe.
Does it mean for some key words is my domain name and web hosting O.K. and for some not?
So if I have a .com on US hosting, I can create a nameserver on example.com.au as dns1.example.com.au and I'm in Australia only searches?
What about load balancing with a .co.uk secondary nameserver? I'm not sure, but the more I think about it the more I doubt it. I'd love someone to confirm either way.