When Christian missionaries came to Japan they taught the Japanese many things. A lot of which they would not have wanted to. The introduction of guns by the Portuguese altered warfare in Japan and led to an intense warring period which ended with the establishment of the Tokugawa shogunate. That's more the Portuguese than the missionaries specifically. Of the teachings from the missionaries what stuck the most was Crucifixion is a torturous and a terrible way to die so let's use it a lot.
Crucifixion, called Haritsuke in Japanese, was used in Japan before and during the Tokugawa Shogunate. The condemned was hoisted upon a T-shaped cross. Then, executioners finished him off with spear thrusts. The body was left to hang for a time before burial.
In 1597, twenty-six Christians were nailed to crosses at Nagasaki, Japan. The executions marked the beginning of a long history of persecution of Christianity in Japan, which continued until the United States of America and other Allies defeated Japan at war in 1945, ending World War II.
The Japanese really do not understand Christianity. They are not really religious people by western standards of religion and their religion has different theologies, for example they are polytheistic instead of monotheistic. Some of their views on Christianity are pretty weird. There is, for example, a Japanese legend that claims that Jesus escaped Jerusalem and made his way to Aomori in Japan where he became a rice farmer. More information on that can be found here: The Japanese Jesus Trail.