I answered a previous question here about Christian missionaries in Japan, their involvement in Japan's domestic affairs and Japan's persecution and eventual suppression of the Catholic faith, which persisted throughout the Edo period. You may find more context about all of this in the link above.

It should be noted that the Tokugawa Shogunate tolerated the Protestantism of the Dutch, who didn't link trade to conversions. They were also forbidden from proselytizing. They became the favored European trading partner due to this, while the Portuguese would fall out of favor because of aggressive Jesuit evangelization in Japan.