I'm assuming you have a Mac that you're running iTunes on, and if that is the case then all you need to do is download the iBooks app for Mac from the Mac App Store. It will import the ebooks from iTunes and you can then manage them from there (they still sync through iTunes but it will work properly).
Thanks for your reply chasm I have already downloaded the iBooks app to my Mac. The books appear there as well as in iTunes and my iPad3. However they will not sync through to my iPad Mini or my iPhone 5.
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