First Zach, let me tell you how thrilled I was to visit the aikiweb site and find your question listed under the active forum threads. I was even more delighted to find out that an aikido practitioner from another country is the one interested. The local aikido community here in Israel is relatively small but quite active.
Now to the question discussed. Amir Krause counted most of the dojos in Israel, but thorough as Amir is, somehow he failed to mention the Seidokan affiliated dojos in Israel.
There are at least 5 such dojos:
2 in Jerusalem, 1 in Maa'le Ha-chamisha, 1 in Rishon Le-zion and 1 in Tel Aviv.
Some info regarding these dojos may be found in this link
I hope all the information gathered here provides a suitable answer to your question. And... if by any chance you happen to visit Israel, you are more than welcome to visit the dojo I practice, in Holon, not far from Tel-Aviv.
Oops, thought you were in the Aikikai list (and now found out I was wrong).
This brought me to think of the Ki-aikido association too, I seem to recall hearing they have one dojo in Israel around Aco, but I could not find any mention of it.
Zach, if you know of other associations, mention them and we can check.
Good luck with your research (could you give some more details about it?).