A similar approach to the one proposed by Anthon - to use Latex - is to try a much simpler, relatively basic way of editing the text where you also markup (similar to how we edit these questions and answers). One of the well used formats is called markdown. Here's a blog post by an author who switched to using markdown instead of Word or other document writing tools http://ianhocking.com/2013/06/22/writing-a-novel-using-markdown/
And you might find the service offered by leanpub helpful. They:
Because the files are textual in nature they're easy to manage and track using source control software such as Mercurial, Git, etc. Text based 'diff' software utilities make changes easier to track e.g. to compare updates between English and Japanese versions of your book.
What they don't seem to do is offer any way to easily allow you to edit two versions of a chapter (etc) in parallel. Nor do they provide an easy way to publish the 'same' book in different languages. Here's a suggestion:
Import the English version of the book and split the book's contents into separate text files, one per chapter. Create a second 'mirror' book on leanpub, this one set to Japanese. For each chapter in the English version, copy the text into the relevant folder for the Japanese version of the book. I'd also change the filename slightly e.g. to chapter1.jp.txt for the Japanese language version and you might even decide to do the same for the English language version e.g. chapter1.en.txt so they're unambiguous and easy to recognize.
As you update the text in the respective file for either language, use a 'diff' tool http://en.wikipedia.org/wiki/Diff to easily see the change(s) you're making. Then apply similar changes to the equivalent file in the other language.
Note: you don't need to actually publish with leanpub, but you can. And you retain copyright of what you write (unless you choose to assign copyright, etc).