Restaurants in Japan are quite outdated in terms of dietary restrictions or food allergies. Kosher is actually not widely known in Japan so please clearly inform restaurants/hotels/ryokans what you can and cannot eat in advance. Below are restaurants that offer kosher meals in Tokyo.
<Roppongi, Ebisu>
FALAFEL BROTHERS
Address
5-1-10 Roppongi, Minato City, Tokyo
<Shibuya>
Kuumba du falafel
Address
23-1 Shinsencho, Shibuya City, Tokyo
<Ebisu>
TA-IM
Address
1-29-16 Ebisu, Shibuya City, Tokyo