During the 16th and 17th centuries, Christianity was seen as a threat; the religion of obstructing the authorities, antisocial behavior and intolerance towards the established religions, by Japan's political authorities, so much so that it was banned.
The Japanese Christians forced to trample on Christ
Just watched the movie "Silence" about this.
Unlike China, etc, Japan kept itself free from any full on European colonialism.
Japan would much later, after Admiral Perry's "famous" or "infamous" visit, align itself politically with England. Doing so allowed them to do their own colonization.
The Shogunate leaned towards a policy of “controlled isolationism,” rightfully concerned about growing imperialism on the part of European powers in Asia. They saw how especially Portugal and Spain worked with the Jesuits in using christianity and firearms as a wedge to gain a political foothold in Japan, and eventually decided to close that door and purge themselves of this pernicious foreign influence.