1 Week Itinerary in the Goto Islands, Nagasaki
The Goto Islands - where Christianity and Buddhism coexist and beautiful beaches abound.
This summer I took a trip to one of Japan's true hidden gems - the Goto Islands, nestled in the serene waters of Nagasaki Prefecture. The islands are places of rich history, and unspoiled beaches - hidden spots where one can easily lose sense of time.
I explored charming fishing villages and soaked in the lush greenery, and explored ancient Christian sites that told tales of resilience and faith.
If you want a tour in Nagasaki central before heading to the Goto Islands, we offer one (which can be customised), click here.
Where are the Goto Islands and how do you get there?
The Goto Islands are situated off the western coast of Kyushu, easily reached from Nagasaki or Fukuoka Airports. There are also ferries and high-speed boats running from Nagasaki and Sasebo Ports.
What are the Goto Islands?
The Goto Islands are a remote group of islands in Nagasaki. They comprise of over 140 islands, of which about a dozen are inhabited. There you will find quiet beaches with crystal clear water, lush foliage, and churches hidden away in remote hamlets and mountainsides.
The Goto Islands have an interesting history as during the 16th century the islands became a refuge for persecuted Christians fleeing the Tokugawa shogunate's ban on the religion. Many of these "hidden Christians" continued to practice their faith in secret, and their legacy can still be seen today in the form of ancient churches and Christian relics scattered across the islands. These historical sites are part of the "Hidden Christian Sites in the Nagasaki Region," a UNESCO World Heritage listing that recognizes their cultural significance.
The islands boast not only a rich history but they also have wonderful nature, from dramatic cliffside views to white-sand beaches. They boast some of the richest marine biodiversity in Japan, making them a popular spot for snorkelling and diving.
My one-week Goto Islands itinerary:
Day 1 - Depart Tokyo
We took a morning flight from Tokyo to Nagasaki Airport. From there, we took an airport bus to Nagasaki Port. At the port they have a restaurant where we ate a quick lunch before boarding the high-speed ferry to Fukue Island. The high-speed boat takes 1.5 hours, while the ferry takes 3+ hours, so we chose the faster option. The high-speed boat is more easily cancelled in bad weather so bear that in mind. We were lucky but the following day, the boat was cancelled.
After checking into the hotel, we walked to Bukeyashiki Samurai Street and the City Museum. The museum is a building designed like a castle surrounded by the surviving castle moat. Inside the building is a museum relating to the history of Fukue and the castle. More interesting was the Bukeyashiki Samurai Street, which was where the samurai class lived during the Edo era. There are some walls, gates and structures that still survive, and the street is pleasant to stroll around and there is a visitor's centre where you can buy souvenirs.
Day 2 - Fukue Island
After picking up our rental car, we first went to Mount Onidake, an extinct volcano that offers panoramic views of the island and surrounding seas. As a New Zealander, I loved this mountain as it was green and grassy, unlike most of Japan's mountains which are thickly covered in trees and bush. Sheep grazing would not have been amiss here. From the carpark you can walk up to a lookout, or hike even further to the top for amazing 360-degree views of the island. It's very beautiful, but be warned, it's extremely windy so hold onto your hats! If you're travelling with kids, you might need to carry toddlers a bit but my six-year-old happily ran around and climbed the mountain easily.
Making the most of the car, we drove to several viewing spots like the Abunze Coastline, where you can see a volcanic landscape jutting out from the coast, easily reached down a short trail.
We paid a visit to Kojushi Beach, where there was an interesting shop where the owner was making sea salt by burning logs and evaporating the water. Sadly due to rough waves, the beach was closed, but it looked really nice.
For lunch we stopped at a seafood restaurant called "焼き小屋くうかい". It's suitable even for people who don't like seafood, as they have many options. The owners were really friendly and you could opt to grill the seafood on the table right in front of you, although we did not.
Being on an island, of course we wanted to go to the beach, so after lunch we headed to Takasaki Beach to try our luck. This beach was not touristy, and only locals were swimming there. There was a small facility with drinks and a 100-yen hose which you could use to rinse off, but otherwise nothing. The water was not so clear on the beach area as a typhoon was coming closer, and it was a bit choppy, but still many people were swimming. There was a long pier and on one side was the beach, and the other side was a much deeper area where boats were moored. In that section, the water was amazingly clear and cool and I actually enjoyed swimming there, although do so with caution as you cannot reach the bottom.
To end the day, we made our way to the scenic Gyogasaki Park and the historic Mizunoura Church. Gyogasaki Park is perched atop a cliff and offers stunning panoramic views that are particularly breathtaking at sunset. The park's serene atmosphere, coupled with the sound of waves crashing against the rocks below, makes it a perfect spot for quiet reflection. Just a short drive away, we visited Mizunoura Church, a simple yet poignant testament to the island's Christian heritage. This quaint church, with its white façade and peaceful surroundings, stands as a reminder of the hidden Christians who once worshiped here in secret.
Finally we visited Dozaki Church, built in 1908 and being one of the oldest surviving churches. It has a museum inside so you can learn all about the history of the church and hidden Christians. To get there you have to park and walk along a quiet inlet to reach it so it feels very peaceful and secluded.
Day 3 - Fukue Island
We started the day with a view at the Osezaki Cape and the Osezaki Lighthouse where the shining blue ocean and cliffs offered us stunning scenery.
Nearby is the Imochiura Church, which is a lovely brick building with a freshwater spring where you can fill your bottle. Inside was hot and stifling, so I didn't spend long inside, but it was a good place for reflection. In other seasons it must be more bearable inside.
From there we went to Takahama Beach, which is considered one of Japan's top 100 beaches and has full facilities available. It was indeed a beautiful beach, with a wide white-sand shoreline and clear water. However an even more beautiful spot was yet to come (read on!).
We paid a brief visit to Kusuhara Church, a brick church is designed in the Gothic style which is the second oldest church in lower Goto, behind Dozaki Church. It was interesting but you could only enter the foyer and there was a plastic screen blocking you from seeing much.
That night the island was having their local summer matsuri (festival), so the centre of town was alive. There are a few connecting main streets that make up the town centre, and they were closed to traffic and there were many stalls, entertainment and games. With talk about Japan's aging population rife, I was surprised to see so many kids and young families, but Fukue Island seems very much alive. It was a nice and cozy festival which added to the holiday feel.
Day 4 - Naru Island and Nakadori Island (Shinkamigoto)
We started the day by taking a short ferry to Naru Island, which is a sleepy island without much going on, but which felt very peaceful.
We made a reservation in advance (required) to go inside the Egami Catholic Church, where we were one of only two groups visiting at the time. Egami Catholic Church was registered as a World Heritage Site by UNESCO in 2018 as one of the "Hidden Christian Sites in the Nagasaki and Amakusa Regions." Apparently, a local elementary school was once located where the car park currently sits, and the cathedral was said to have been a playground for the students who left children's graffiti inside the cathedral. When it was registered as a World Heritage Site, UNESCO apparently ordered the graffiti to be removed, but the locals insisted that it remain, so the graffiti can still be seen today.
After the church we drove around to see some viewpoints (Odagawara and Shirotake Observatorys) and Shiwanoura Pond which was by a very peaceful harbour. Some of the roads on the island are not in the best condition so be sure to drive slowly.
From Naru, we took the ferry to Nakadori Island (Narao Port) which is the second most populated island of the Goto Islands. It has even more churches than Fukue and we found it to be more beautiful and idyllic.
For lunch we got bentos to eat outside from a shop called "グリデキッチン" . The food was much nicer than in normal bento boxes, and a good price as well. I recommend going here if you need a quick lunch.
Another beach trip was in order, so we visited Hamagurihama Beach which is a wide white sand beach with lots of little tide pools to splash in when the tide is out. The water is still and clear and there's a platform you can swim out to and jump off. This beach was great for kids and they have changing and shower facilities.
Dinner was at Men's Hamasaki near the beach. It has both tables and tatami seating and a large menu. It was full when we were there so it seems like a popular place, and the food was excellent!
Day 5 - Nakadori Island
The best beach of the entire trip was Hamanna Beach. It was secluded, with no facilities on offer, and only one other family there. The water was absolutely crystal clear and a lovely sparkling blue. This beach felt like a true tropical paradise.
Nearby is the Kurosaki Park Lookout, worth heading to for more spectacular ocean views.
We went to the stone village of Tomosumi. Tomosumi started as a fishing village but after stonemasonry became popular, many villagers switched to that. You can see plenty of remains of the Goto sandstone in the village. Some people still live there so you can stroll quietly around being careful not to disturb anyone, although it did feel like I'd jumped back in time about 60 years, with many houses being shuttered, leaving you to imagine what was once a thriving village.
It being the land of the hidden Christians, more church visits were in order. There was Aoasagaura church with its lovely stained-glass windows, and Akabae church which involved a steep drive up a hillside and a slightly scary parking situation.
We ended the day with more views - the Tsuwazaki Lighthouse and Yagatame Observatory - both with amazing lookouts over the ocean and islands but a very long drive to the tip of the island.
Day 6 - Wakamatsu Island (connected to Nakadori Island)
One of the highlights of the trip was visiting Kiri Church and Kiri Village down in Shinkamigoto. Imagine driving around the coastline and passing through quaint fishing inlet after inlet, all surrounded by sparkling clear blue sea. Kiri Church is perched atop a hill with stunning views of Kiri Village, the most beautiful fishing village I've seen. The church was closed so we could not go inside, but the views made up for it. The water was crystal clear and pleasantly chilled, and I desperately wanted to go for a dip.
From there we drove to Ryukazan Observatory for yet another spectacular view. This trip was all about the views. There were many stairs to reach the top of the observatory, after which we learned that due to tree growth the view was actually better from the carpark.
After that was the most picturesque drive along the coastlines to the Hinoshima Stone Pagodas, located in a tiny village with a surprisingly large elementary school which I suspect is now abandoned (a common theme with schools on the Goto Islands). Over 70 stone pagodas, each with distinct shapes and sizes, are scattered across the windswept sandspit at the southern tip of Hinoshima, a small island near Wakamatsu. Once blanketed by forest, this area served as a hidden burial ground for medieval traders and seafarers. Here, they laid their fallen to rest, commemorated comrades lost at sea, and even erected monuments for themselves, anticipating a similar fate. Most of these pagodas were constructed between the late 1300s and 1400s, during a time when Goto mariners thrived on trade and piracy along the Korean Peninsula and Chinese coasts, selling their rare goods to the elite of Kyoto.
Near these pagodas is a small but beautiful beach where you are unlikely to see other people. The water was shallow stunningly blue and there was a section roped off for swimming, with signs warning you not to go further out as there were stingrays. This beach is just marked on Maps as "若松ディアパーク公衆トイレ".
After lunch it was on to Nakanoura Church. The church, perched on a hillside overlooking the sea, was built in 1925, with its simple, white facade stands in contrast to the deep blue waters below. The church was constructed by the local Christian community, descendants of the hidden Christians who secretly practiced their faith during centuries of persecution. Today, Nakanoura Church is a place of quiet reflection, although we saw many stand-up paddleboarders going past in the water below.
Day 7 - Ojika Island
At the end of the trip, we went to an island which isn't technically part of the Goto Islands, but is just north of them.
That was Ojika Island, a small island of 2500 people which is reached by ferry from Nakadori. To get around we rented a car, but the island is also small enough to explore by bike.
First we stopped at the Ojika History Museum, where one of the staff members happily showed us around in English, teaching us all about Ojika Island. The museum is small but worth stopping at for around 30 minutes to learn a bit about where you are.
After that we went to the Akahama Coast Red Beach, where the sand is not whte but slightly red. It makes a nice photo spot and you can sit and watch the waves crash ashore.
We drove past the Hime no Matsubara, a pine tree avenue that is really pleasant to pass through. I'm always a sucker for green grassy fields, so we also stopped at the Nagasakibana cow pasture to see cows grazing by the cliffside. You could walk on the fields right up to the cows - it felt like New Zealand!
To end the day we visited Shirahama Beach, a small beach with a swing. It was nice and clear and quiet, but the waves were a bit choppy so we didn't swim here. As the day came to a close, we went to Madarashima which is a collection of potholes dotting the cliffside, interesting to see but hold your kids tightly!
After Ojika, we went to Fukuoka by ferry and flew back to Tokyo from there.
If you would like a tour of the Goto Islands, contact us for a custom tour!
