Some cruise ships pass through areas around the islands that are currently embroiled in territorial disputes between Japan and its neighbors.
Japan and Russia never signed a formal peace treaty at the end of WWII, due to a territorial dispute. When cruising around certain parts of Hokkaido, you may be able to spot the islands of Etorofu, Kunashiri, and Shikotan, as well as the Habomai group, known in Japan as the "Northern Territories" and in Russia as the "Southern Kuril Islands." These islands were occupied by the Soviet Union in the final days of WWII. They are still administered by Russia even though Japan still lays claim to them as their own. When cruising certain parts of Okinawa, you may also spot the Senkaku Islands, currently administered by Japan but also claimed by China and Taiwan (or Takeshima as it is known to the Japanese). Japan also claims Dokdo Island, which is currently administered by South Korea. These ongoing disputes flare up from time to time, and the resulting tensions can have a significant impact on the flow of tourists to and from the countries involved.