Maybe if you call the builder he would be happy to come back and fix his mistake?
The average toilet is for a 12 inch rough in (12 in. from wall to center of toilet flange). But sometimes they will fit when only 11 inches is available.
So maybe you’d be lucky enough that a toilet with 10 inch rough in dimension would fit in your 9 inches.
Here’s one of many available with 10 inch rough in: http://www2.kohlerco.com/plumbing/detail.asp?item=9801&prod_num=3432-UR
But if you’re all that lucky, I guess the builder will come back for free.
An alternative would be to move the pipe and flange out three inches and use a normal toilet.
Or just install an offset floor flange that will give you enough for a 10 inch rough in.