Since October 2014 iBooks Author supports direct import of ePUB ebooks to new projects so they can be used to produce iba and ibooks files.
If you for some reason do not have iBooks Author (it's free), you can use the following workaround with iTunes.
When you drag non-DRM protected ePUB to iTunes, your ebook will be imported to your iBooks library. However, you won't be able to download it in IBOOKS format.
These ebooks will then be saved in the location depending on your platform:
Windows: \Users\****\Music\iTunes\iTunes Media\Books
Mac: Users/****/Music/iTunes/iTunes Media/