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Persecution of Christians in Japan

Francis Xavier, the first European to evangelize in Japan, left the country in 1551. With the help of daimyō patrons, the Jesuit missionaries soon gained a considerable number of converts in the island of Kyushu. Their numbers increased during the time of the shogun and Japan’s first unifier Oda Nobunaga. However, everything went downhill when he was succeeded by the second unifier Toyotomi Hideyoshi and his successor Tokugawa Ieyasu. European missionaries were viewed as precursors of foreign invasion, so the persecution of Christians soon started in the country.  These events are recorded on the Bible Timeline Online with World History during this time period.

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Christianity in Japan During the Final Years of the Sengoku Period

Ōtomo Sōrin was a Japanese feudal lord who converted to Roman Catholicism.

In late 1551, Father Francis Xavier left the fledgling Christian community of Japan and entrusted it to fellow Jesuits Father Cosme de Torres and lay brother Juan Fernandez. By then, Christianity only had a frail presence in some areas of the island of Kyushu and Yamaguchi. The suicide of the daimyō Ōuchi Yoshitaka, one of the Jesuits’ earliest patrons, was a blow to the Christian community. The fragile presence of the religion was saved when Xavier befriended the daimyō of Oita (Funai), Otomo Yoshishige (Sorin), before he left Japan for India.

Sorin’s interest in Christianity, however, went beyond intellectual curiosity. As one of the most powerful warlords of the period, he used his friendship with the Portuguese and the Jesuits to import firearms from Macau. He was the Christians’ primary protector in a war-torn country, but it was not until 1578 that he was baptized.

The Christian presence in Oita increased as years passed. In 1555, Sorin allowed the Portuguese physician Luis de Almeida (who was supported by the Jesuits) to establish an orphanage in Oita. It was followed by a hospital in 1557, and it was not long before Oita became the Jesuits’ headquarters in Japan. Christian missions, however, were still largely confined in Kyushu and growth was limited. It did not help the Jesuits’ cause when the missionary Gaspar Vilela started to burn Buddhist books and destroy images he found offensive.

One of the first daimyōs to convert to Christianity was Ōmura Sumitada. The Portuguese and the Jesuits had overstayed their welcome in Hirado, so they were forced to find a friendlier port in 1561. They approached Ōmura Sumitada, the daimyō who ruled Yokose-ura in Nagasaki Prefecture and tempted him with firearms and other products brought by Portuguese ships. In exchange, he would have to convert to Christianity and allow the Jesuits to preach in his land. The daimyō readily agreed and he was baptized two years later.

Christians who were expelled from Hirado and Yamaguchi soon flocked into Nagasaki where they established a community. By the early 1570s, Nagasaki had become the base of Portuguese merchants and of the Jesuit mission. During a conflict with other daimyōs in 1574, the Jesuits pressured Ōmura to repay their “favors” by ordering everyone to convert to Christianity and drive out anyone who refused to do so. They also asked him to destroy Buddhist and Shinto images in his territory and forbid his people from worshiping idols.

Ōmura agreed to do as the Jesuits ordered. In November 1574, he ordered his men to raze or burn Shinto and Buddhist shrines in his territory. Around 60,000 inhabitants of his domain were forced to convert to Christianity. The instant addition to their numbers made Father Torres and fellow Jesuit missionary Gaspar Coelho ecstatic.

 The Age of the Shoguns and the Start of Persecution

By the end of the Sengoku period and the rise of Japan’s unifier Oda Nobunaga, there were around 150,000 Christians in Japan. Oda Nobunaga disdained Buddhism because of the fighters of the Ikko sect who continually frustrated his efforts to unify Japan. Although he never converted to Christianity, the pragmatic daimyō chose to befriend the Jesuits. He allowed them to build a church and establish a school (the Seminario) in Azuchi. There the Jesuits instructed the upper-class children in Christian history, literature, and Latin. His patronage did not last as one of his vassals rebelled against him in 1582. He committed suicide and his enemies destroyed the daimyō’s Azuchi Castle along with the Jesuits’ Seminario.

Oda Nobunaga was succeeded as the unifier of Japan by Toyotomi Hideyoshi, one of his most capable and influential generals. He had established friendly relations with the Jesuits which he had granted certain privileges in 1586. He invaded Kyushu in 1587 and quickly brought to heel the daimyōs of the island.

Father Gaspar Coelho, Vice-Provincial of Nagasaki and Superior of the Jesuit mission, sailed to meet the victorious general off the coast of Hakozaki. Their first meeting on July 19, 1587, occurred without an accident, but the atmosphere became menacing five days later. To Father Coelho’s surprise, Toyotomi Hideyoshi issued an anti-Christian edict and an ultimatum for the missionaries to leave Japan within 20 days.  

The daimyō’s anti-Christian edict was not without reason. First, the forced conversions of Buddhists and Shinto practitioners did not sit well with him. He also compared the Christians to the followers of the Ikko sect and insinuated that they might one day rebel against him. In addition, he accused the Jesuits of being complicit to the trading of Japanese slaves to China, Korea, and India. Of all these accusations, only the third one was unfounded.

Father Coelho had no choice but to submit to the powerful daimyō. Toyotomi Hideyoshi then took Nagasaki and appointed an administrator for the city. He ordered the destruction of churches, and although none of the missionaries left Japan, they were forced to be discreet when it came to their activities in the future.

This tenuous tolerance of Christianity would be broken in 1593 when a group of Spanish Franciscan missionaries from the Philippines arrived in Kyoto. According to the Jesuits, their Franciscan rivals became so fervent in their evangelization that they fueled the suspicions of Toyotomi Hideyoshi.

The situation would only worsen when the Manila galleon San Felipe was wrecked at Urado Bay in December 1596. The daimyō ordered his men to confiscate the cargo of the Spanish ship, but they were alarmed when they found some weapons along with the gold and bolts of silk. The alarmed guards arrested the ship’s navigator and then tortured him. The navigator “admitted” that the Spaniards prepared for the conquest of a country by sending their friars first to convert its people and establish churches. After softening the country’s defense with religion, a full-scale military invasion would then follow.

The navigator’s “confession” spelled disaster for both Franciscans, Jesuits, and Japanese converts to Christianity. Upon hearing the confession, Toyotomi Hideyoshi ordered his men to execute twenty-six Christians (seventeen Japanese lay brothers, six Franciscans, and three Jesuits) in Nagasaki. He also renewed the edict that prohibited the evangelization activities in his realm. Hideyoshi’s preoccupation with the invasion of Korea, however, narrowly saved the Christian community of Japan. The country’s second unifier died on September 15, 1598, and his generals were soon forced to wrap up the long but unproductive invasion of Korea.

Hideyoshi’s generals soon scrambled to fill the power vacuum their master left behind. During the Battle of Sekigahara in 1600, Tokugawa Ieyasu, one of Oda Nobunaga’s generals, defeated the faction led by the Toyotomi clan. He then went on to become Japan’s most powerful daimyō. The arrival of the English navigator-turned-retainer William Adams became a turning point for Catholics in Japan. Adams, a Protestant, stoked the shogun’s fears by insinuating that the Portuguese missionaries were forerunners of a foreign invasion.

An incident between two Christian officials of the shogun would seal the fate of the religion in Japan. During the shogun’s reign, a Christian daimyō named Dom Protasio Arima Harunobu tried to reclaim some properties he lost during the reign of Toyotomi Hideyoshi. A fellow Christian official named Okamoto Daihachi then told Harunobu that he could serve as an intermediary between the daimyō and the emperor. Harunobu readily believed Okamoto and bribed him to facilitate the return of the properties.

Okamoto Daihachi, however, only forged some papers. In 1612, the frustrated Harunobu later learned that the transaction was fraudulent and that Okamoto’s superior was unaware of the incident. He immediately appealed to Tokugawa Ieyasu for redress who then ordered Okamoto’s execution. Before his death, Okamoto accused Harunobu of conspiring to kill the commissioner of Nagasaki whom the shogun had previously appointed. 

The punishment came swiftly for Harunobu. The shogun sent him to exile and later ordered his execution. The incident made Tokugawa Ieyasu more suspicious of Christians. Vigorous persecution of Christians followed, and he soon forbade the presence of the religion in his realm. Harunobu’s son, Dom Miguel Arima Naozumi, tried to pacify the shogun by renouncing his faith and forcing his people to do the same. This strategy did not work, and he was reassigned to another fief as punishment.

In 1614, the shogun finally issued the “Statement on the Expulsion of the Bateren.” Missionaries were driven out of Japan, but some stubbornly remained in the country and were forced to go underground. Conversions and baptisms continued even under the shadow of persecution. More adventurous (and foolhardy) missionaries, meanwhile, smuggled themselves into the country and continued their missionary activities.  

Two years later, the shogun ordered his officials to intensify the persecutions so that Christianity would be eradicated as soon as possible. Imprisonments, tortures, and executions centered in the Christian cities of Hizen and Nagasaki. In 1622, fifty-five European and Japanese Christians were executed in the city of Nagasaki.

By 1639, Japan had become isolated. The shogunate drove the Portuguese merchants and all European missionaries out of the country. Dutch merchants were the only ones allowed to trade in Tokugawa Japan. By 1660, three thousand Japanese Christians had died and the rest were forced to renounce their faith. Only a few hardy adherents remained but they were forced to practice their religion in secret.


Picture by: Unknown author京都国立博物館蔵, Public Domain, Link

Elisonas, Jurgis. The Cambridge History of Japan: Early Modern Japan. Edited by John W. Hall. Vol. 4. Cambridge: Cambridge University Press, 2006.

Toon, S., and David Michell. The New International Dictionary of the Christian Church. Edited by J. D. Douglas and Earle E. Cairns. Grand Rapids, MI: Zondervan Publishing House, 1996.

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