Japan has historically been wary of outsiders ever since dealing with the Portuguese Christian missionaries which were attempting to convert the Japanese population to Christianity in the late 1500s and early 1600s. The leader at the time correctly assumed that Japanese culture and way of life would be destroyed if the foreigners were allowed to go into the country.

You'll see that 'xenophobic' claim made often. It's true to an extent. Japan just wants to protect their culture and way of life. They don't want to end up like the US now.