Christianity’s Bloody History in Japan

Japan has had a vexed relationship with Jesus ever since European missionaries arrived on its shores. Banned until 1873, successive leaders have asked whether love of the ‘two Js’ is compatible.

Japanese Christians re-enact the crucifixion of Jesus Christ, c.1880s. Chronicle/Alamy Stock Photo.
Japanese Christians re-enact the crucifixion of Jesus Christ, c.1880s. Chronicle/Alamy Stock Photo.

Early in 1638, Japan’s Tokugawa shogunate found itself mired in a combination of embarrassment and crisis. Requests were coming into its headquarters in Edo – present day Tokyo – for troops to lay siege to a castle on the coast of Kyushu, Japan’s southernmost main island. The castle had been captured by rebels, and to make things worse they were not even samurai. They were peasants – Christian peasants.

Christianity had been a feature of Japanese life for almost a century by this point. Back in 1549, the Jesuit missionary Francis Xavier arrived in Kyushu to begin what he was confident would be a fruitful mission. It was generally believed by Europeans of his era that the gospel had once been preached across Asia by Thomas the Apostle and others. So when the Jesuits began to evangelise in India, China and Japan, hitching a ride on Portuguese merchant ships, they were on the look-out for signs of some lingering awareness of Christian truth.

They found it in Japan – or, at least, they thought they did. An informant named Anjirō, who had fled Japan aboard a Portuguese ship after being accused of a murder, told of a country where altars, bells, rosaries, incense, statues and paintings were all used in religious worship. There were monasteries, too, where monks lived communal lives of prayer, chanting and fasting. Everyone knew about heaven and hell, having heard about them from a holy man who had lived long ago. This man had preached a single creator God, had given commandments – including prohibitions on killing and theft – and had lived somewhere to the west beyond China.

The arrival of Christian missionary Francis Xavier in Japan. Japanese painted screen, 16th century.
The arrival of Christian missionary Francis Xavier in Japan. Japanese painted screen, 16th century. CPA Media Pte Ltd/Alamy Stock Photo.

God’s arrival

Anjirō was describing Japanese Buddhism. But Xavier and his colleagues were sufficiently impressed with what seemed like an ancestral memory of Christian teachings and practices to use a Japanese name for the celestial Buddha – ‘Dainichi’ – for ‘God’ when they arrived in Kyushu and began to preach, using a Japanese text prepared for them by Anjirō.

All did not go entirely to plan. The Jesuits found that poverty lacked the religious resonance in Japan that it possessed in Europe, where the founders of the Jesuit Order had once gone about in sackcloth. To dress in this way when preaching before a Japanese feudal lord – or ‘daimyō’ – was regarded as insulting rather than inspiring. Nor did the Jesuits understand the East Asian culture of gift-giving. Xavier was refused an audience with the emperor in Kyoto because he arrived bearing neither official letters nor proper presents.

As they did elsewhere in the world, the Jesuits in Japan set out to learn about the culture in which they were working and to adapt themselves where possible. They began to dress better for their appointments with senior daimyō, and to make artfully clear that generous treatment towards missionaries would be rewarded with visits by Portuguese merchants – who were engaged in a lucrative and eminently taxable trade between Japan, China, India and Europe.

The Jesuits meanwhile laid ‘Dainichi’ to rest, once they realised that this was a different ‘god’ and religion entirely. They took to eating with chopsticks, taking small bites and avoiding meat. They no longer kept live animals in their homes and they washed their clothes regularly. They began to build their residences in the Japanese style, including a room dedicated to the tea ceremony. And once they had acquired the basics of the language they set about trying to understand Zen Buddhism: both its ‘men of great meditations’ and the arts with which the religion was associated: poetry, calligraphy and painting.

For many Japanese, the Jesuits discovered, Zen was either too austere or too elite. They preferred forms of Buddhism in which it was necessary only to call on the name of a particular Buddha – Amida – in order to be saved. This reminded the Jesuits of Lutheranism back in Europe: a deluded belief, placed by the devil in the hearts of lazy or desperate people, that there existed an easy path to salvation. They set about trying to reach these people through spectacle, donning rich vestments – gold cloth, brocade and velvet – and competing with their Buddhist rivals to offer magnificent processions and funeral ceremonies. Palanquins and silk banners were employed alongside torches, holy water, crucifixes and Latin prayers. Such were their hopes for the potential of beauty and emotion to soften people’s hearts that some of the Jesuits even kept records of which attendees cried during services.

Warring states

By the early 1580s, these efforts, alongside those of Japanese catechists, had yielded somewhere in the region of 150,000 converts, out of a population of around 15 million. It was a small but significant proportion, all the more so when converts were grouped largely in one place – Kyushu – and included powerful daimyō. One of these, Ōmura Sumitada, baptised ‘Dom Bartolomé’, gifted the Europeans a natural harbour. What began as a modest fishing village turned into the international trading town of Nagasaki: a hub for merchants and missionaries alike, home to Jesuit schools and a printing press.

The Jesuits had begun to overcome one of the major barriers to Japan’s conversion – the perception of Christianity as culturally foreign – only, now, to run into another: politics. These were turbulent times in Japan. The emperor’s power had waned centuries before, replaced by that of military governments – or shogunates – based first in Kamakura and later in a district of Kyoto. That system, too, had broken down in the 1400s, and Japan had since been a country at war with itself: rival daimyō fought, negotiated and double-crossed one another in an effort to expand their domains.

Oda Nobunaga, initiator of the unification of Japan in the 16th century. Woodblock  print by Utagawa Kuniyoshi, 1830.
Oda Nobunaga, initiator of the unification of Japan in the 16th century. Woodblock print by Utagawa Kuniyoshi, 1830. Heritage Image Partnership Ltd/Alamy Stock Photo.

The ultimate prize, in what came to be known as the ‘warring states’ era, was to reunify Japan. Those who sought to achieve that feat were acutely aware of the danger posed to them by religious groups, large Buddhist sects in particular, who boasted great wealth, warriors and a certain hold over sections of the population. The most important warlord of the 1560s, 1570s and early 1580s was Oda Nobunaga, and he owed much of his success to ruthless treatment of his Buddhist rivals. In 1571, he sent 30,000 troops storming up Mount Hiei, home to the Tendai sect. They burned down its temple complex – comprising around 3,000 buildings – and slaughtered the monks and families living there and nearby. A little over ten years later he laid siege to the headquarters of another sect, Jōdo Shinshū, resulting in yet more bloodshed.

Where Buddhists had stood in Nobunaga’s way, Christians threatened the ambitions of his successor Hideyoshi Toyotomi. When Hideyoshi set out to bring Kyushu into his emerging Japanese state in the late 1580s he was horrified to learn of its strong links with foreign powers: Portugal and Rome. He had no particular dislike of Christianity, and was an admirer of Portuguese fashion. But to be told that the Jesuits could help him bring Kyushu to heel, and then later that the real aim of some missionaries was to prepare the way for European colonisation, made it clear that Christianity posed a serious political threat. Hideyoshi responded to that threat with a series of persecutions, culminating in the crucifixion of the ‘twenty-six martyrs’, as they became known, on a hill overlooking Nagasaki in February 1597.

Hideyoshi died in 1598. Two years later the third and final great unifying figure of this period, Tokugawa Ieyasu, won an epoch-making victory at the Battle of Sekigahara. He tolerated Christianity at first, hoping to build trading relationships with European powers – particularly the Spanish in Manila and Mexico. But Japanese Christians continued to bother him and his dynastic successors. Shogunal officials heard that when Christians were put to death for a crime, other Christians would turn up to sing hymns in their honour. This was an insult to the shogunate: they were flaunting their lack of fear of arrest. And it seemed to go hand-in-hand with their worship of a man, long ago and far away, who had been tried and executed by a legal authority.

The Shimabara Rebellion

This apparent theme in Christianity, of holding secular authority ultimately second to something or someone greater, became vividly clear to the shogunate in the autumn of 1637, when there arose, in parts of Kyushu, a dangerous combination of failed harvests, heavy taxation and a perception of religious persecution. The trouble started in Shimabara domain, around 25 miles east of Nagasaki. It was under the control of a non-Christian daimyō called Matsukura Katsuie, who had become infamous for making impossible tax demands and dishing out terrible punishments when these were not met. One of these, the ‘Mino dance’, involved dressing a recalcitrant farmer in his winter straw coat, tying his hands behind his back, and then setting him on fire. Others were thrown into snake pits, sliced with bamboo saws, boiled in sulphurous hot springs and forced to watch as their wives or daughters were hung naked, upside-down, in public.

By December 1637, people in Shimabara and neighbouring Amakusa – both heavily Christian areas – had had enough. Tens of thousands of them rose up, some of whom made their way to the largely abandoned Hara Castle and began to refortify it. Religion was secondary to impoverishment and anger in fomenting what became known as the Shimabara Rebellion, but Christianity undoubtedly gave it a sense of purpose. A young Christian boy named Amakusa Shirō became the movement’s figurehead, preaching and assisting in the saying of Mass in Hara Castle. A Christian flag was flown: white silk, with a black chalice in the centre, a communion wafer hovering above and angels in adoration on either side. Banners with red crosses were hung from the parapets.

Hara Castle,  site of the Shimabara Rebellion by Japanese Christians, c.1800.
Hara Castle, site of the Shimabara Rebellion by Japanese Christians, c.1800. Historic Collection/Alamy Stock Photo.

Given the gulf that supposedly separated warriors from peasants, in terms of military training and social status, the occupation of Hara Castle ought to have been very short-lived. Worryingly for the shogunate, it began to drag on. Ninjas were sent into the castle as spies, but at least one of them was caught because he understood neither the local dialect nor the Portuguese Christian words used by the rebels. Attempts were made to dig under the castle, but the rebels heard the noises and filled the tunnels with smoke, faeces and urine. A full-frontal attack was tried and repelled.

In the end, an expanded Tokugawa force of between 100,000 and 150,000 men had to be sent to Hara Castle to bring this humiliating episode to a close. Even then it took dwindling supplies – and no doubt morale – within the castle to give government troops the advantage that they needed. By April 1638, the rebels were so low on food and ammunition that a large group led by Amakusa left the castle under cover of darkness to see what they could steal from Tokugawa forces. They were spotted and hundreds were killed. When their stomachs were cut open to get a look at their most recent meal, only seaweed, barley and leaves were found. Not a single stomach had rice in it.

Confident of victory, the Tokugawa troops attacked, scaling the castle walls in full armour – or so painted-screen reproductions of the siege would have us believe – and a three-day battle began. Samurai found themselves fighting half-starved rebels, many with little more than cooking pots and cauldrons to use as weapons. By the time it was over, everyone in the castle had been put to death, barring just a few who managed to escape. The heads of men, and the noses of women, were taken as trophies and presented by each warrior to be counted.

Concerned that would-be rebels around Japan might take inspiration from a story about an untrained peasant rabble holding off tens of thousands of warriors, the shogunate recorded the rebellion as religious in nature – with foreign powers involved in fomenting and supporting it. This was a smart move for the shogunate, but a devastating one for Christians in Japan. Foreign missionaries were banned, as were all Europeans except for the Dutch – who agreed to limit themselves to trade. An existing prohibition on Christianity was strengthened and rigorously enforced. Those suspected of harbouring lingering affection for Christianity were made to attend a Buddhist temple and tread on a Christian image, to prove that they had nothing to do with the outlawed faith.


Christianity survived in Kyushu nonetheless, but the so-called ‘hidden Christians’ had such sparse contact with the outside world that over the decades and centuries their religion developed into something quite distinct from the teachings of Francis Xavier. After a new, modernising regime took the place of the Tokugawa shogunate in 1868, the missionaries who began to flood in – Protestant, Catholic and Orthodox – regarded themselves as starting almost from scratch.

For a while, progress seemed to be good. The old ban on Christianity was lifted in 1873, and by the early 1890s Protestant Christian numbers in Japan stood at more than 30,000. Particularly encouraging for the missionaries was that a sizeable number of former samurai discovered a new ‘lord’ in Jesus Christ – finding, in his teachings, something close to Confucian ethics.

Japanese Christian leaders began to emerge, urging foreign missionaries to take a back seat in the Christianisation of Japan. Too many were bata-kusai (‘stinking of butter’): unable to differentiate between Christian conversion and the adoption of Western lifestyles and mores – including heavy consumption of dairy products. If Christianity were once again to overcome the sorts of cultural barriers faced by the Jesuits back in the 16th century, space would have to be created for authentically indigenous forms of the faith to develop. One of Japan’s new Christian leaders, Uchimura Kanzō, sought to bypass Western Christendom and discover cultural affinities between contemporary Japan and parts of the ancient Middle East. The Apostle Paul, he suggested, had been a ‘true samurai’: independent, fiercely loyal and placing little value on money.

A church under construction in Tokyo, c. 1926. Finnish Heritage Agency (CC BY 4.0).
A church under construction in Tokyo, c. 1926. Finnish Heritage Agency (CC BY 4.0).

Such efforts enjoyed only partial success, and Christianity’s fortunes in Japan soon foundered once again on the question of divided loyalties. Uchimura had insisted that there existed no contradiction in his love for ‘the two Js’ – Jesus and Japan. But Japan’s rise to great power status by the turn of the 20th century had been fuelled by intense political rhetoric about the Japanese as a single, united community, resisting Western colonial power. When the rhetoric of resistance turned to actual conflict against Russia in 1904 some in Japan were inclined to paint it as a war of religion – or at least to use it as an opportunity to make Japanese Christians think again.

The prominent philosopher Inoue Tetsujirō asked whether the recent rise of pacifism among the Japanese – some of whom did not see the need for war with Russia – might be linked to the cultural inroads being made, of late, by Christianity. Jesus Christ had taught a set of values that seemed antithetical to Japan’s present interests, from a naïve rejection of using force against enemies, to the placing of his god above family and nation. Christianity seemed so far-fetched – a religion, in Inoue’s view, accidentally kicked off by a young girl trying to explain away an illegitimate pregnancy – that perhaps Japanese who followed it were motivated by a secret preference for England or America.

Japan’s Christians responded by making increased efforts to demonstrate their patriotism. Christian publications eulogised soldiers who supposedly quoted scripture to one another in the thick of the action. On the home front, Christians donating to the war effort sought to be conspicuous in their generosity. Japanese Christianity managed to survive over the decades that followed, but the late 19th-century surge of interest was not repeated. For all that Uchimura Kanzō had sought a truly ‘Japanese’ form of Christianity, much of the interest in what Western missionaries had to offer had been bound up with a broader exploration of Western languages and cultures. Once that faded, and new generations of Japanese had passed through schools whose government-mandated curricula taught an older set of values – rooted in Shintoism, Buddhism and Confucianism – Christianity took up a place on the country’s cultural margins. It was tolerated as an aspect of modern Japan’s cosmopolitanism, rather than being regarded as central to its identity.

‘Born Shinto, die Buddhist’

The real religious winner of the Russo-Japanese war was a civil religion of officially sanctioned emperor worship, which intensified after victory over Russia in 1905 and was used to powerful effect by Japan’s military as it deepened its hold on the country’s politics in the 1930s. It helped, indirectly, to thwart a third effort at Christianising Japan during the Allied Occupation from 1945 to 1952. Missionaries and bibles flooded in – the latter sometimes used, rumour had it, as a source of paper for rolling cigarettes – but Americans and Japanese alike were haunted by memories of the brutalities and massacres visited on Asia by an imperial mindset linked to state-sponsored Shinto and emperor-worship.

A procession carries the right arm of Francis Xavier through the streets of Nagasaki, 9 June 1949.
A procession of Japanese Christians carries the right arm of Francis Xavier through the streets of Nagasaki, 9 June 1949. Associated Press/Alamy Stock Photo.

In 1947 a new American-authored constitution separated church from state, and the teaching of religious doctrines in schools was banned. Political progressives in Japan warned that values like devotion and self-sacrifice were partly to blame for the rise of militarism: too few people had been willing to question authority. These were now replaced, across much of the political spectrum and in Japan’s mainstream media, by secularism, self-responsibility, scientific knowledge and a certain scepticism about authority. When ‘new religions’, as they came to be called, emerged in postwar Japan, many had roots in Buddhism rather than Christianity and were conspicuous for their focus on worldly survival and success rather than grander, metaphysical speculations and promises.

Towards the end of the Second World War, Japan’s leaders had briefly worried that a combination of suffering, poverty and deep disillusionment might drive people to embrace communism. Similar fears persisted in the early years of the occupation. But by the mid-1960s, the majority of Japanese were settling for quiet, comfortable lives over radical and disruptive ideas – whether political or religious. Set alongside postwar Japan’s values, this left Christianity labouring under a series of unhelpful – albeit conflicting – associations: foreign, dangerous, worryingly exclusive in its claim to truth, unscientific and all-in-all surplus to requirements.

There may come a fourth wave of Japanese interest in Christianity, but that seems a long way off. One sign of a religion’s cultural sway is its hold over life and death: people’s willingness to accept its mediation, perhaps also its interpretations, when life arrives or passes away. In Japan, the notion of ‘born Shinto, die Buddhist’ has been true, now, for long enough that it has become a cliché. Newborns and children are celebrated with festivities at Shinto shrines, while funerals are very often conducted at Buddhist temples.

The role of Christianity in marking great life events in Japan is limited to ever-popular Christian-style marriages, their aesthetics owing much to on-screen Western weddings and Disney princesses. After centuries of bitter and sometimes bloody controversy, Christianity has at last found a safe, stable place for itself in Japan – but not the one Francis Xavier had in mind when he sailed for Kyushu all those years ago.


Christopher Harding is a cultural historian and broadcaster based at the University of Edinburgh. His most recent book is The Japanese: A History in Twenty Lives (Penguin, 2022) and he writes about Asia’s impact on Western life at