Due to Japan is an isolated island nation, without any land boundary with other state, maritime transport has a very important role in Japan.
Then, due to lack of own natural resources, Japan totally depends on importing natural resources; crude oil, iron and etc, from the natural resource producing countries. These natural resources are all carried to Japan by vessels.
Actually it was the one of the main reason why Japan had started invading other countries in the Pacific due to obtaining the natural resources. The invasion spurred when US, UK, China and the Netherlands made an embargo against Japan. The Japanese imperial army and navy attacked British Malaya, Dutch East Indies and the Pearl Harbor in December 1941.
Not only cargo, but also vessels are important to carry passengers for the international routes. Japanese had to either cross the Pacific or Sea of Japan to go to Europe until the introduction of regular international flights after the WWII. Ships carrying cargo and passengers were connecting Yokohama and Vancouver/Seattle. The people took the ship to Vancouver or Seattle and changed to a train connecting the East coast - New York. Then, again taking a ship from NY to UK. The people who had to go to France, Germany or other continental nation, they had to cross the Dover strait too. The other route was taking trains to Tsuruga, Moji or Shimonoseki stations, and cross the Sea of Japan and head to Vladivostok, Dalian or Pusan and change to the trains which connect to Trans Siberian railway. The fastest route was Shimonoseki-Pusan-Changchun-Moscow-Berlin. Leaving Tokyo at 15:00 on 1 June, arrived in Moscow at 17:00 on 13 June, Berlin at 09:23 on 15 June, Paris at 06:43 on 16 June and London at 16:55 on 16 June. Actually the passengers could buy a one way ticket(a single paper) from Tokyo to London.
Still international routes are available in Japan. Major routes are Shimonoseki - Pusan, Osaka/Kobe - Shanghai, Hakata - Pusan(hovercraft!) and Sakaiminato - Vladivostok. If you are afraid of airplane and have plenty of time, why not taking Trans Siberian railway and the ship from Vladivostok?