According to The Australian Oxford Dictionary Sixth Edition, the primary spelling is 'web site' as two words. The single word spelling 'website' is considered a secondary spelling. If you check the Macquarie Dictionary Fifth Edition the preferred spelling is 'website' as a single word and 'web site' as two words is a secondary spelling variation. When the authoritative references don't agree it can be hard to determine the preferred spelling in Australia, but this does happen more than one might expect.
Many editors refer the 'Style Manual: For Authors, Editors and Printers, 6th Edition' which is an Australian Government publication and what we find is the following in the section relating to computer and internet terms. We find the sentence 'For example, lower case appears to be the predominant usage for web site, which is also often seen as one word.' The only problem with the Style Manual is the sixth edition was published in 2002 (reprinted with corrections in 2003, reprinted in 2006, 2007, 2008 and 2010) and whilst the language can change slowly in some areas, some areas change much more quickly.
Using these three resources the weighting would appear to favour 'web site' as two words and that is currently what I use in my dictionary work. The two word variation 'Web site' with the capitalised first letter is not mentioned in the above references. As can be seen by the sentence in the Style Manual the lower case usage has become predominant, so at least we can rule out 'Web site' as the preferred Australia English spelling. However, 'web site' and 'website' need examined further.
Based on various searches of the internet for Australian sites, using different search engines, using a variety of filters, in all cases the predominant usage is 'website'.
I find one of the hardest things we can do with our own use of the language is to change the spelling of a word when we've used the one spelling for so long. In this case my earlier research indicated 'web site' to be the preferred spelling, but now a few years later this isn't the case. For me I have to bite the bullet and adjust my site according. The online service Word Check will be updated today and the dictionary files for Microsoft Office and Internet Explorer will be updated and released as time permits.
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