Japan is one of the few nations which have over 10 million inhabitants and surrounded by sea only, no land border with any neighboring country. If you consider island nation which has more population than 100 million, Japan is one of the two countries in the world, together with the Philippines.
Therefore Vessels are very important meaning of transportation for Japan. 99.8 percent of international trades are relying on vessels. If you count on per person, Japan is importing and exporting approximately 9.8 tons per year by vessels. Imported goods are carried to Japanese ports which can be found any prefectures which are next to the sea. Then transferred to factories or other facilities. Carrying 1 ton of beef from Australia would cost JPY 1.30 per 100g but JPY 1.45 from the port to the butcher.
Then, there are many types of vessels in Japan. Therefore you can see a lot of ships and boats at Japanese harbors. If you visit Sasebo, Yokosuka, or Maizuru, you can see also self defense force's vessels too. By the way, there are also several international maritime routes connection foreign ports by ships.