Francisco Xavier reached Japan on 27 July 1549

Francisco Xavier reached Japan on 27 July 1549
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Francisco Xavier portrait by probably Kano Gensuke, found out in 1919, Osaka. The house old hidden Christians.

In Malacca in December, 1547, Francisco Xavier met a Japanese named Anjiro. Anjiro had heard from Francisco in 1545 and had travelled from Kagoshima to Malacca with the purpose of meeting with him. Having been charged with murder, Anjiro had fled Japan. He told Francis extensively about his former life and the customs and culture of his beloved homeland. Anjiro helped Xavier as a mediator and translator for the mission to Japan that now seemed much more possible. "I asked [Anjiro] whether the Japanese would become Christians if I went with him to this country, and he replied that they would not do so immediately, but would first ask me many questions and see what I knew. Above all, they would want to see whether my life corresponded with my teaching."

Anjiro became the first Japanese Christian and adopted the name of 'Paulo de Santa Fe'.

Europeans had already come to Japan: the Portuguese had already landed in 1543 on the island of Tanegashima, where they introduced the first firearms to Japan.

He returned to India in January 1548. The next 15 months were occupied with various journeys and administrative measures in India. Then, due to displeasure at what he considered un-Christian life and manners on the part of the Portuguese which impeded missionary work, he travelled from the South into East Asia. He left Goa on 15 April 1549, stopped at Malacca and visited Canton. He was accompanied by Anjiro, two other Japanese men, the father Cosme de Torrès and Brother João Fernandes. He had taken with him presents for the "King of Japan" since he was intending to introduce himself as the Apostolic Nuncio.

Shortly before leaving he had issued a famous instruction to F. Gaspar Barazeuz who was leaving to go to Ormuz (a kingdom on an island in the Persian Gulf, now part of Iran), that he should mix with sinners:

And if you wish to bring forth much fruit, both for yourselves and for your neighbors, and to live consoled, converse with sinners, making them unburden themselves to you. These are the living books by which you are to study, both for your preaching and for your own consolation. I do not say that you should not on occasion read written books . . . to support what you say against vices with authorities from the Holy Scriptures and examples from the lives of the saints.

Francisco Xavier reached Japan on 27 July 1549, with Anjiro and three other Jesuits, but he was not permitted to enter any port his ship arrived at until 15 August when he went ashore at Kagoshima, the principal port of the province of Satsuma on the island of Kyushu. As a representative of the Portuguese king, he was received in a friendly manner. Shimazu Takahisa (1514–1571), daimyo of Satsuma, gave a friendly reception to Francisco on September 29, 1549, but in the following year he forbade the conversion of his subjects to Christianity under penalty of death; Christians in Kagoshima could not be given any catechism in the following years. The Portuguese missionary Pedro de Alcacova would later write in 1554:

In Cangoxima (Kagoshima), the first place Father Master Francisco stopped at, there is a good number of Christians, although there is no one there to teach them; the shortage of laborers has prevented the whole kingdom from becoming Christian.

Hosted by Anjiro's family until October 1550. From October to December, 1550, he resided in Yamaguchi. Shortly before Christmas, he left for Kyoto but failed to meet with the Emperor. He returned to Yamaguchi in March, 1551, where he was permitted to preach by the daimyo of the province. However, lacking fluency in the Japanese language, he had to limit himself to reading aloud the translation of a catechism.

Francisco was the first Jesuit to go to Japan as a missionary. He brought with him paintings of the Madonna and the Madonna and Child. These paintings were used to help teach the Japanese about Christianity. There was a huge language barrier as Japanese was unlike other languages the missionaries had previously encountered. For a long time Francis struggled to learn the language. Artwork continued to play a role in Francisco’ teachings in Asia.

For forty-five years the Jesuits were the only missionaries in Asia, but the Franciscans also began proselytizing in Asia as well. Christian missionaries were later forced into exile, along with their assistants. Some were able to stay behind, however Christianity was then kept underground as to not be persecuted.

The Japanese people were not easily converted; many of the people were already Buddhist or Shinto. Francis tried to combat the disposition of some of the Japanese that a God who had created everything, including evil, could not be good. The concept of Hell was also a struggle; the Japanese were bothered by the idea of their ancestors living in Hell. Despite Francisco’ different religion, he felt that they were good people, much like Europeans, and could be converted.

Xavier was welcomed by the Shingon monks since he used the word Dainichi for the Christian God; attempting to adapt the concept to local traditions. As Xavier learned more about the religious nuances of the word, he changed to Deusu from the Latin and Portuguese Deus. The monks later realized that Xavier was preaching a rival religion and grew more aggressive towards his attempts at conversion.

With the passage of time, his sojourn in Japan could be considered somewhat fruitful as attested by congregations established in Hirado, Yamaguchi and Bungo. Xavier worked for more than two years in Japan and saw his successor-Jesuits established. He then decided to return to India. Historians debate the exact path he returned back by, but due to evidence attributed to the captain of his ship, he may have travelled through Tanegeshima and Minato, and avoided Kagoshima due to the hostility of the Daimyo. During his trip, a tempest forced him to stop on an island near Guangzhou, China where he saw the rich merchant Diogo Pereira, an old friend from Cochin, who showed him a letter from Portuguese being held prisoners in Guangzhou asking for a Portuguese ambassador to talk to the Chinese Emperor in their favor. Later during the voyage, he stopped at Malacca on 27 December 1551, and was back in Goa by January, 1552.