Japan in the 1500s had a greater fragmentation in religious organization than did Western Europe – the fragmentation the Roman Catholic Church wanted to prevent. The ease with which people drifted in religious belief had produced in Japan a great variety of sects – sects that split into factions. Into the 1500s in Japan there was no central religious authority that had the power and influence to confine any drift in religious ideas.
Political power lay with the shoguns – hereditary military chieftains and political dictators – and they believed that they had the right to exercise control over religious organizations. Freedom of worship was not a well developed concept in Japan. But the shoguns were less interested in religious concepts in general than were members of the Catholic hierarchy or John Calvin.
The Ashikaga shogunate fell in 1573, and the new central government was led by Toyotomi Hideyoshi. He created greater centralized control than had the Ashikaga shoguns. Buddhist monks became subject to control by the warrior class. Buddhist temples were put to work keeping the population under control. People were obliged to register as a parishioner at a Buddhist temple, and the temple was obliged to record whether their parishioners espoused belief that was dangerous. Most temple leaders bent to the will of the Hideyoshi's regime, and those temples that cooperated received in return protection and political and economic support. Buddhist monks willingly became servants of the military government – in general. There were always the stubborn who did not want to go along.
The Buddhist Nichiren sect was among those who came under pressure from the government. Nichiren temples were many, and most of them capitulated. Nichiren who did not formed another of Japan's sub-sects: the Fuju-fuse sub-sect. They chose independence from the government and denounced those Nichiren who chose subservience. The Fuju-fuse movement gradually gathered momentum, provoking a strong reaction from the government.
The state demanded that Fuju-fuse temples issue receipts for the state resources (land, water, roads and the like) that they were using. The shogunate responded to Fuju-fuse recalcitrance by making its parishioners hinin (non-persons), and their temple leaders were threatened with exile. Some Fuju-fuse leaders tried escaping the temple and preaching in the streets, but authorities moved against this. The Fuju-fuse were outlawed altogether. Believers in the importance of the priests tried to leave their temple and preach in the streets, but that was also forbidden. A few chose to live as outlaws, hiding and holding services at night. Some were arrested, exiled or sentenced to death together with their families. In 1668, a Fuju-fuse leader, Nikkan, and five followers and their families, including children, were arrested – thirty-four persons. Nikkan and some of his followers were beheaded. Others, including the women and children, were exiled. In 1691, sixty-three more Fuju-fuse leaders and eleven followers were exiled, which means that they were sent to live on what were then remote islands, such as Nii-jima, barely 3 square miles and 80 miles off into the Pacific Ocean from the port of Yokohama, or Miyake-jima, a volcano island about 5 miles across and 95 miles from Yokohama.
Also, in the latter half of the 1500s, Christians felt the sting of Japanese government persecution – hardly enhancing respect for freedom of worship among the few in western Europe aware of it and struggling with the issue.
A few Nestorian Christians may have wandered to Japan in the fifth century, but it was in the latter half of the 1500s that Christianity had its substantial arrival in Japan. Roman Catholic missionaries in the 16th and 17th centuries wanted quality converts. But they were also business-minded and interested in commerce. There was some hope that Japan would be a jumping off point for Christianizing China, the most populous of the "heathen" countries. The missionaries are said to have supplied medicine and care for the sick for people left destitute by war and that this earned them praise among the Japanese.
But their aggressive ways and sense of superiority annoyed the ruler, Toyotomi Hideyoshi, who declared Japan "the land of Kami (God)" and ordered the expulsion of the Jesuit missionaries. Hideyoshi was also concerned with control, but interested too in trade with the Christian Europeans. His edict was not enforced for a decade. Power passed to his son, who, in 1597, had 26 Christians executed and 24 Christians arrested, among them 19 Japanese. The prisoners' left ears were chopped off and the prisoners were paraded through Kyoto's streets and surrounding countryside while onlookers taunted them. Arriving in Nagasaki, all 24 prisoners, plus two Jesuits who had come to defend them, were chained to crosses, crucified, stabbed with spears and left to hang for 80 days. Learning of their deaths two years later, Pope Pius the IX declared them martyrs.
None of the Christians had recanted or denounced their faith and this had impressed a few Japanese. New converts were recruited and the city of Nagasaki remained the center of Christian activity. In 1614 all European priests were ordered to gather at Nagasaki for deportation. Christian churches were ordered destroyed and Japanese converts ordered to renounce their Christianity. Being a Christian was made a capital offense. More Japanese Christians were executed, and Japanese Christians, a tiny minority among their fellow countrymen, pursued their Christianity in secret.
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