Question

why the distribution of the population island is not uniform throughout japan

Answer 1

This is so as places such as Japan are habitable only around a narrow coastal fringe. Only 5% to 10% of the land can support any significant population. So the actual population density of either Japan  is ten to twenty times the apparent density, i.e., population divided by land area. The population density in 90 to 95 percent of the land is virtually nil.