Are you looking to cultuvate your ninjas for additional power? You can obtain relatively quickly by doing survival trials. Another way to get cultivation runes can be from group merchamt shop, specifically Arena exchange rewards!! =)

You'll have a lot of them later, so don't waste credits to buy them.
The fastest way to get them is doing the Survival Trial.

http://image.prntscr.com/image/2ac332f085664e7bb3abaea54a0680a5.png

If you are referring to cultivation runes, just have a little patience. You'll have all you need by the mid 70s, and swim in them by the 80s.