I've moved your question to the InDesign EPUB forum.
It would help if you told us what version of InDesign you're using, and whether you're creating a reflowable EPUB or a fixed layout EPUB.
Hi Mr Steve Werner...
according to your replay on question... i am using InDesign (CC2014)
Have you tried Adobe Arabic which is an open type. Usually open type fonts work well with ePub. Let us know. Also, are you using the English-Arabic version of Indesign. You have access to it through the Creative Cloud desktop app.