Nagasaki: The Hidden Hub of Christianity in Japan

In the 16th century, Christianity was introduced to Japan via Nagasaki. Many Japanese converted to Christianity, however, the religion was soon outlawed, forcing believers to go underground. Known as Hidden Christians, they continued to secretly practice their faith in the remote parts of Nagasaki, creating a unique religion that continues to this day. In this article, we’ll explore the turbulent history of Christianity in Japan and take you through Nagasaki’s fascinating Catholic landmarks - including UNESCO World Heritage Sites!

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Japan’s Gateway to the World: The History of Nagasaki

Once a small fishing settlement, Nagasaki rapidly developed into a bustling port city following the arrival of Portuguese traders in the mid-16th century. At this time, Japan was still a collection of feudal states under the control of different samurai lords, rather than a unified country. Nagasaki was part of the domain of lord Omura Sumitada, the first Christian daimyo, who offered Nagasaki as a fiefdom to the Portuguese Jesuits, giving them a strong foothold in feudal Japan.

However, during Japan’s period of isolationism, which began in the early 17th century, the Portuguese were expelled, and only a limited number of Dutch and Chinese traders were allowed to remain on Nagasaki’s man-made islands of Dejima and Shinchi respectively to continue international trade. This continued until the end of Japan’s seclusion in the mid-1800s, after which Nagasaki became a major shipbuilding city until it was devastated by an atomic bomb at the end of WWII. Today, Nagasaki has bounced back as a vibrant and cosmopolitan city with a complicated yet fascinating past.

A Brief Guide to Religion in Japan

The two dominant religions in Japan are Shinto and Buddhism. Shinto is native to Japan, and is seen in records as early as the 8th century, with some iconography even traced back to the prehistoric Yayoi Period (400 BC to 300 AD). Shintoism has no founder, scripture, or single god. Instead, it is believed that spirits and deities called “kami” inhabit many things, particularly elements of nature such as trees, mountains, and rivers. Kami are enshrined at Shinto shrines, while humans also become ancestral kami when they pass away, worshiped at altars in family homes.

Buddhism was introduced to Japan from China in the 6th century. Buddhism follows the spiritual teachings of Buddha, a holy figure who lived in southern Asia sometime between the 6th and 4th centuries BC. Though there are fundamental differences between Shintoism and Buddhism, they often overlap. For example, in Japan, Buddha has come to be seen as a deity much like Shinto kami, and it’s common to see Shinto shrines and Buddhist temples side by side.

Minority Religions in Japan

Shintoism and Buddhism remain by far Japan’s most popular religions, and many Japanese believe elements of both. However, there are also a number of minority religions in Japan that are practiced by immigrants as well as Japanese converts. Of these, it’s thought that there are between 1-2 million who practice Christianity in Japan, making it the largest minority religion in the country, accounting for roughly 1% of the population. Among them are a small group known as “Hidden Christians,” who are descendents of early Catholics who secretly practiced in areas around Nagasaki while the religion was outlawed between the 17th-19th centuries.

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The Timeline of Christianity in Japan

Christianity first formally arrived on the shores of Japan in 1549 in what is now Kagoshima by Catholic missionaries from Portugal and Spain. The most prominent of these missionaries was Francis Xavier, a Spanish Jesuit who spent just over two years preaching Christianity in Japan.

Nagasaki Becomes the "Rome of Japan"

To support their religious activities, missionaries engaged in trading commodities, such as silver, porcelain, and silk. In 1570, the port of Nagasaki was officially granted permission to trade with merchants from overseas, and parts of the land were given to the Jesuits. These missionaries built a number of churches in Nagasaki, which became known as the “Rome of Japan.”

By 1579, around 130,000 people in Japan had converted to Catholicism, heavily influenced by the conversion of several high-ranking samurai, including the ruling Omura Sumitada, the first Christian daimyo. While there were many Christian converts spread across Japan, Nagasaki and the greater Kyushu region remained the religion’s main stronghold.

Growing Distrust of Christianity in Japan

In the 1580s, Toyotomi Hideyoshi became the leader of a reunified Japan, and quickly grew wary of the intentions of Christian missionaries. Concerned that missionaries were using religion as a way to extend their empire into Japan, Hideyoshi’s suspicions were heightened by acts of destruction committed by Christian samurai against Shinto shrines and Buddhist temples.

In 1587, fearing that the Christian samurai were attempting to convert Japanese people by force, Hideyoshi passed laws that effectively banned Christianity in Japan and expelled all priests and missionaries. However, these laws were initially not strictly enforced in Nagasaki, as the lucrative trade with Portuguese was prioritized over religious concerns. The city still had several Catholic churches, though followers were careful to practice discreetly. Towards the end of the 16th century and beginning of the 17th century, it is estimated that up to 300,000 people had converted to Christianity in Japan.

The Crackdown on Christianity in Japan During the Edo Period

However, by the late 16th and early 17th centuries, crackdowns became increasingly severe. In 1597, 26 Christian missionaries were publicly crucified in Nagasaki, following revelations that other missionaries had used Christianity as a way to colonize territories overseas. These martyrs became recognized as saints by the Catholic Church in 1862.

The Shimabara Rebellion and the Ban on Christianity in Japan

Under the rule of the Tokugawa Shogunate during Japan’s Edo Period (1603-1868), punishments for practicing Christianity in Japan became even more brutal, and Catholicism was banned entirely in 1614. Over the following years, Christian churches in Nagasaki were destroyed and remaining missionaries were deported, and all Japanese Christian converts who did not renounce their religion were ordered to be tortured and executed.

The persecution of Christians became even more severe following the Shimabara Rebellion in 1637-38. The rebellion came in response to heavy taxes set by the local ruling lord, along with oppression of local Christians. Around 30,000 people seized Hara Castle near Nagasaki, mostly made up of Catholic peasants and disaffected “ronin” samurai. In response, the shogunate sent over 120,000 troops to retake the castle, and 37,000 rebels and sympathizers were beheaded following the insurrection.

The Hidden Christians of Nagasaki

With Christianity in Japan completely outlawed, and facing execution as punishment for following their religion, many Catholics in Nagasaki were forced to hide their faith. A large number fled to some of the remote islands around Nagasaki, particularly the Goto Islands, where it was easier to continue to practice in secret. Such followers came to be known as “Hidden Christians.”

With no formal organization, Nagasaki’s Hidden Christians developed their own unique form of Catholicism. Icons of Christ and the Virgin Mary were often made from images of Buddhist or Shinto gods, such as Kannon, the Buddhist Goddess of Mercy, so that their true religious affiliation wouldn’t be detected. Catholic prayers were also adapted so that they sounded like Buddhist chanting.

Despite an initial continued crackdown, the ban on Christianity in Japan was finally lifted in 1873 after over 250 years by the Meiji Government following the end of the Edo Period. However, even after liberation, many of Nagasaki’s Hidden Christians continued to practice in the same secretive way with their own unique customs. Some residents of regional Nagasaki still identify as Hidden Christians, following the faith as their ancestors did when the religion was prohibited.

Hidden Christian Sites in the Nagasaki Region

In 2018, twelve Christian sites in Nagasaki, along with Sakitsu Village in neighboring Kumamoto Prefecture, were granted UNESCO World Heritage status. Below is an overview of the main Nagasaki Hidden Christian UNESCO lineup, plus some other related spots worth checking out along the way!

Oura Cathedral

Nagasaki’s Oura Cathedral is said to be the oldest church in Japan, and is one of the most popular World Heritage Sites on this list. It was built by French missionaries in 1864 to serve the growing number of foreign Christians who had settled in Nagasaki, and is dedicated to the 26 Catholic martyrs killed in 1597. Shortly after Oura Cathedral was built, several Hidden Christians came to the church to declare their faith, revealing how the religion had been preserved for hundreds of years.

Oura Cathedral was also the first Western-style building in Japan to be declared a National Treasure. Beside the church is the Former Latin Seminary, built in 1875 to train Japanese clergy. Students of the seminary were instrumental in reaching out to Nagasaki’s Hidden Christian communities following the lifting of the ban on Christianity.

Remains of Hara Castle

It was the brutal crushing of the Shimabara Rebellion at Hara Castle that ultimately forced Japan’s Christians into hiding. Today, the scenic ruins of World Heritage Site Hara Castle mark the site of the rebellion, which lasted for an impressive four months. Also on the site is a statue of Amakusa Shiro, the leader of the Shimabara Rebellion, as well as his tombstone.

Kasuga Village and the Sacred Places in Hirado

The island of Hirado played a significant role in the development of Christianity in Japan. Francis Xavier himself spent time here to help establish a devout Catholic community. The island’s World Heritage Site of ​​Kasuga Village is one of the oldest Christian settlements in Japan, and there are still graves of the country’s earliest Catholic converts remaining today. The bucolic landscape is lined by photogenic rice terraces running from the ocean to the mountains, with the grand Mt. Yasumandake, an object of worship by the Christians, in the backdrop.

Also off the coast is the tiny uninhabited island of Nakaenoshima, another part of the UNESCO collective, and worshiped by Hidden Christians as a site of martyrs. While you can’t get on the island, cruises are available to see it from the ocean.

While not part of the World Heritage Site, Hirado is also home to a handful of beautiful historic churches. This includes the red-brick Hoki Church, built in 1898, which boasts a gorgeous interior and colorful stained glass windows, as well as the elegant white Himosashi Church, standing over the streetscape in the center of Hirado Island, built in 1929.

Shitsu Village and Ono Village, Sotome

The village of Shitsu in Sotome was home to another community of Hidden Christians and is now part of the World Heritage Site. Located on the coast around 30 km northwest of Nagasaki City, many Christians fled here to continue following their faith in secret without fear of persecution. After the ban on Christianity in Japan was lifted, Father de Rotz, a French priest, built the Shitsu Church in Sotome in 1882 for the now-liberated Catholics.

Shitsu Church’s distinctive exterior made with layers of mortar gives it an authentic Japanese look, slotting in with the native architecture. On the bell tower at the front stands a statue of the Virgin Mary, which was ordered from France when the church was built. Next to the church is the former Shitsu Aid Center, which was opened by Father de Rotz as a vocational training facility for women to learn essential skills such as cooking, farming, and textile-making.

Just a 10-minute drive away from Shitsu is Ono Church in Ono Village, also a World Heritage Site. The village was home to another settlement of Hidden Christians, who practiced under the guise of Shintoism. After persecution ended, the simple, rustic Ono Church was erected in 1893 by Father de Rotz and locals using stones fashioned from a unique mixture of sand, lime, clay, and basalt rock.

Just to the southeast of Shitsu Church is the red brick Kurosaki Church (not part of the UNESCO site), which was built by members of the local Catholic community in 1920 to a design laid out by Father de Rotz. The surrounding village of Kurosaki was also the setting for the novel Silence by Shusaku Endo, which was later turned into a film by Martin Scorsese.

Kuroshima Island

Kuroshima, located off the coast of Sasebo, north of Nagasaki City, is another island where communities of Hidden Christians settled. It is a UNESCO World Heritage Site, and is most famous for its symbol of Kuroshima Church, a grand, red-brick Romanesque building with a spectacular interior inspired by designs in Europe at the time. Painstakingly constructed by parishioners, it was finished in 1902, and flaunts a number of embellishments like beautiful stained glass windows.

The Goto Islands

The Goto Islands are a chain of five main islands off the coast of Nagasaki. There are dozens of sites associated with Christianity in Japan spread across the islands, including historic churches that were built after the ban was lifted. It’s the islands of Hisaka and Naru that are home to Goto’s World Heritage Sites.

Hisaka Island hosts the Hamawaki Church on the southeast of the island, and the Old Gorin Church on its east coast. The chalk-white Hamawaki Church overlooks a beautiful bay, while the rustic, wooden Old Gorin Church was relocated to its current spot from Hamawaki in 1931. On Naru Island, the small Egami Church in Egami Village stands as one of the best examples of early wooden churches on the Goto Islands, blending a strong Western influence with the local building techniques of the time.

Though not a member of the UNESCO World Heritage collective, another of Goto’s most famous religious sites is Dozaki Church, a striking red-brick building constructed in 1908 in the north of the main island Fukue.

Plus, the town of Shinkamigoto, which covers the upper Goto Islands, is also the location of another two of the area’s most picturesque historic churches - Aosagaura Church and Oso Church. Both sit in the north of Nakadori Island, designed in similar classical brick styles overlooking two of the island’s beautiful bays. There is also the white weatherboard Nakanoura Church, built in 1925 in the center of the island, and the stately Former Tainoura Church, first constructed in 1903.

At the bottom of Goto’s Wakamatsu Island is the “Christian Cave,” where a Christian family hid to avoid persecution. They were sadly discovered and executed after smoke from their fire was spotted, making it a sacred spot today. It is only accessible via boat tour.

Kashiragashima Island

Kashiragashima Island is also under the jurisdiction of Shinkamigoto, and sits just off the coast of Nakadori Island. It served as another safe haven for Christians in Japan, who outwardly appeared as Buddhists while continuing to practice Catholicism. The island was originally used to house sick people, and was thus avoided by others, making it a great hideaway. Kashiragashima’s main attraction is Kashiragashima Church, a unique dome-topped sandstone church built in 1919, part of the UNESCO World Heritage Site.

Remains of Villages on Nozaki Island

Nozaki Island is located just to the north of the Goto Islands. During the rule of the Tokugawa Shogunate, many Catholics in Nagasaki fled here, forming two communities, Nokubi and Funamori, and publicly appearing to follow Shintoism at the island’s Okinokojima Shrine. Despite its World Heritage status, today Nozaki Island is largely abandoned, with the Former Nokubi Church the highlight of what remains of its past as a hub of Christianity in Japan.

Other Notable Christian Sites in the Nagasaki Region

There are dozens more Christian sites in Nagasaki besides the locations granted UNESCO World Heritage status. Here is a selection of other historic Christian landmarks worth adding to your Nagasaki itinerary.

The Monument to the Twenty-Six Martyrs of Japan

This monument and museum is dedicated to the 26 Christians killed in 1597, and was built on the site of their execution. Perched on a hill in central Nagasaki, just a five-minute walk from Nagasaki Station, it features a striking mural of relief sculptures depicting all 26 martyrs, unveiled to commemorate the 100th anniversary of their canonization. Behind the monument is the Twenty-Six Martyrs Museum, which documents the history of Christianity in Japan and Nagasaki.

Santo Domingo Church Museum

Excavations carried out while building an elementary school revealed the remains of the former Santo Domingo Church in the center of Nagasaki, which was destroyed in 1614. The Santo Domingo Church Museum now stands over the foundations, which can be viewed from a raised walkway. There are also displays of many fascinating artifacts, including roof tiles decorated with crosses.

Urakami Cathedral

Construction began on Urakami Cathedral in 1895 and finished in 1914. The church was built on the same site in Nagasaki City where suspected Christians in Japan were forced to step on images of Christ and the Virgin Mary in order to “prove” that they were not followers of the outlawed religion.

The original Urakami Church was the largest cathedral in East Asia, until it was destroyed by the atomic bombing of Nagasaki on August 9, 1945, detonating just 500 meters from the church as a mass was about to take place. Urakami Church was rebuilt on the same site in 1959, and there remains a number of statues and sections of the original structure on display, including a bell that withstood the blast and continues to ring to this day.

Kaminoshima Church

Kaminoshima is a reclaimed island located around a 15-minute drive south of Nagasaki Station. Perched on a hillside overlooking the sea, the Kaminoshima Church boasts a resplendent chalk-white facade, built in 1897. Near the church and facing the sea is a tall white statue of the Virgin Mary, great for photos.

Hotel in Nagasaki: THE GLOBAL VIEW Nagasaki

Uncover the Fascinating History of Nagasaki’s Hidden Christians

The sites explored in this article are all reminders of the extraordinary and difficult lives of the Japanese Christians, who secretly followed their faith in fear of persecution for over 250 years in Nagasaki’s remote areas. Their significance has been acknowledged with the granting of UNESCO World Heritage status, and each site presents its own unique slice of the fascinating story of Christianity in Japan.

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Top image: PIXTA

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The information in this article is accurate at the time of publication.

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About the author

James Davies
Originally from Cardiff in the UK, James has been working as a freelance writer since moving to Japan in 2020. Having first visited Japan in 2013, he has now visited all of the country’s 47 prefectures. A lover of sushi, sumo, and sake, when he's not writing, James is either exploring Tokyo or planning a trip to a new corner of Japan.
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