Duck is a common meat in Europe but not so in Japan. It is quite hard to get in ordinary supermarkets and therefore duck are eaten mostly in restaurants. However, there is a long tradition to eat duck in Japan.
Although it is not so common to eat duck in Japan, it does not mean that duck dish is worthless to try during your stay in Japan. Most common duck dish is duck hot pot, "Kamo nabe" and Kamo namban soba noodle. Kamo means duck in Japanese. By the way, Namban means spring onion = scallion.