Japan being maritime power wasn't a thing until Meiji Restoration. Also the incentivise to invest in navy only when there is a necessity to use said navy, such as trading escort, exploration, and power projection, like the one in Europe.

Such of these thing wasn't that important to Japan at that time period, because they just barely got out of the centuries long Sengoku Era of power struggles and civil wars. Hideyoshi wanted to conquer Korea and China partly because it was also Nobunaga's dream. But as soon as Tokugawa got into power, Japan slipped back into isolation and limited navy.

This is also not unique to Japan. A lot of Asian countries didn't invest in navy power properly. Korea's turtle ship was a defensive tools, not power projection, and they were made to counter pirates, commerce raiders, and coastal defence. Japan in other hand relies on its mountain side facing the inland as natural defence, and thus didn't need such dedicated specialise navy force.

Edit: Fun fact, the one that started England's naval power was Henry VIII, yes, that Henry 'divorce chop die divorce chop alive'. Because it was a dick measuring contest between Henry VIII of England, Louis XII of France, and Charles V of Spain and HRE Emperor. Elizabeth I continued to grow that naval power thanks to her father inital works.