Many temples in Japan have treasure houses of varying degrees of interest. Of these, the National Treasure Museum at Kofukuji Temple is probably the best despite its understated location and exterior - it is easily overlooked on a visit to Kofukuji. The museum has a great collection of Buddhist art that includes the three-faced, six-armed Ashura Statue, one of the most celebrated Buddhist statues in Japan.

Located in Nara Park, the outstanding Nara National Museum is an old fashioned, highly educational museum about Buddhist statues. The museum displays a permanent collection of Japanese Buddhist art and religious artifacts. It also hosts annual exhibitions of treasures from nearby Todaiji Temple every autumn.

This museum's star attraction is its beautiful garden, which is widely considered to be one of Japan's best. But the museum also houses an outstanding exhibition of Japanese paintings and tableware, most notably a large collection of paintings by Yokoyama Taikan.

The Kubota Itchiku Art Museum presents a collection of outstanding kimono created with the highly labor-intensive tie-dyeing technique by Kubota Itchiku. The intriguing museum buildings and surrounding gardens further enhance the appeal of this museum near Mount Fuji.

The National Art Center Tokyo (Kokuritsu Shin-Bijutsukan) in Roppongi is one of Japan's largest museums. The museum maintains no permanent collection but hosts excellent exhibitions that change periodically. The facility's futuristic building is part of the attraction.

The Miho Museum features structures of interesting designs integrated into the natural surroundings. The museum captivates with a theme of contrasting steel, glass and warm stone, complemented by panoramic views of the surrounding valleys. The museum's exhibits consist of works from ancient civilizations such as the Egyptians, Romans, and various Asian cultures.

The Otsuka Museum of Art is the largest museum in Japan. It houses a huge collection of life-size reproductions of Western art masterpieces from antiquity to the 20th century, including works by Michelangelo, El Greco, Goya, Monet and Picasso.

Located on the top floors of the Roppongi Hills Mori Tower, the Mori Art Museum hosts interesting, rotating exhibitions of contemporary art. The exhibitions nicely complement the great aerial views that can be seen from the observatory located on the floor below.

As its name suggests, the 21st Century Museum of Contemporary Art in Kanazawa features a variety of avant-garde art works within a fascinating building of modern interior decor. It exhibits intriguing creations of acclaimed contemporary artists from Japan and all over the world. The museum frequently hosts temporary exhibitions of recently-designed art pieces as well.

The Teshima Art Museum is one of the most intriguing contemporary artworks in Japan. Standing amongst terraced rice fields, the simple concrete structure stimulates its visitors' senses with the play of water drops on a concrete surface. The location of the museum on a rural island makes it even better with an added rustic charm.

The Chichu Art Museum, designed by renowned architect Ando Tadao, is a very special modern art museum built mostly underground into a hillside overlooking the southern coast of Naoshima Island. The museum building itself is a work of art, cleverly utilizing natural light to illuminate the artwork, thereby creating a viewing experience that is heavily influenced by the surrounding natural environment.

The Inujima Seirensho Art Museum tastefully incorporates an art gallery into the ruins of a copper refinery. The gallery showcases a number of intriguing artworks, including a tunnel of mirrors.

The Tokyo National Museum in Ueno Park houses one of the best and largest collections of national treasures and important cultural items in the country. Interesting temporary exhibitions are held here, as well.

The Edo-Tokyo Museum vividly illustrates the past of Tokyo (formerly Edo) and gives a good introduction to the metropolitan city that we see today. In an interactive way, visitors are able to experience and learn about various aspects of earlier Tokyo, such as the way of life of people, Edo Period architecture, cultural heritage, political climate, commercial situation and more.

The Sengukan Museum allows visitors to learn more about the periodic rebuilding of the sacred Ise Shrines. Located at the entrance of the Outer Shrine (Geku), the museum affords views of the elusive main shrine hall from a close distance. The museum's outstanding exhibits include a fourth of a 1:1 replica of the shrine's main building as well as a beautiful 1:20 model of the main sanctuary.

The foremost place in Japan to learn about Ainu culture, Upopoy opened in 2020 as the first national museum dedicated to the history and culture of the Ainu, the indigenous people of northern Japan. It is surrounded by a lakeside park that features some reconstructed, traditional Ainu houses and facilities to experience Ainu culture.

The Hiroshima Peace Memorial Museum reflects upon the dropping of the bomb in 1945 and its outcome in human suffering. The personal details displayed are quite upsetting, and they serve to remind that peace should not be taken for granted. The museum is located in the Peace Memorial Park, a dedication to world peace.

The sobering Nagasaki Atomic Bomb Museum exhibits devastated scenes of Nagasaki after the dropping of the second atomic bomb. Documentaries about the atomic bombing are shown, relating the horrors of war and emphasizing the threat of nuclear weapons and the importance of the peace. Close to the museum is the Nagasaki Peace Park and the iconic Peace Statue.

The Okinawa Peace Memorial Museum commemorates the Battle of Okinawa and serves as a memorial to the people who perished or suffered as a result of war. The museum is part of the Okinawa Peace Park, where many monuments dedicated to both Japanese and foreign casualties of the Battle of Okinawa have been erected.

The Chiran Tokko Museum preserves documents, letters and belongings of the members of the special attack corps (known in English as "kamikaze pilots") during World War 2. The museum does not glorify, but rather serves to remind of the sadness of war.

The Fukui Dinosaur Museum is recognized as one of the top dinosaur museums in the world. The excellent museum is dedicated to dinosaur research and education, and it displays more than 40 dinosaur skeletons. Visitors can learn about how life emerged on earth and how dinosaurs evolved into birds. There is also a hands-on zone where visitors are encouraged to pick up and hold real fossils.

Located in Ueno Park, the large National Science Museum covers both science and natural history with hands-on physics and robotics exhibits. The museum houses an impressive collection of mounted animals and a 360 degree virtual theater.

Also known as the Miraikan, this well done, highly interactive and bilingual science museum in Odaiba includes exhibits about environmental issues, robots, information technology, biology and space exploration.

The Railway Museum showcases an impressive collection of formerly used train cars including steam and diesel locomotives, as well as retired shinkansen (bullet train), passenger and freight cars. The museum recounts the history of railway in Japan, teaches train operation using interesting simulators, and explains railway technology as it evolved over the years.

The SCMAGLEV and Railway Park informs about the advances in high speed rail in Japan. It displays a number of actual trains including historic steam locomotives, world record setting experimental shinkansen and the latest magnetic levitating trains (maglev). The museum also has simulators where visitors can try driving a train or experience the duties of a train conductor in charge of opening and closing the doors.

Located within walking distance of Kyoto Station, the Kyoto Railway Museum covers the history of Japanese railways from steam locomotives to the shinkansen. It is well known for its large collection of steam locomotives.

The Earthquake Memorial Museum commemorates the tragic Great Hanshin Awaji Earthquake of 1995. It educates visitors about earthquakes and disaster prevention through various interactive games, documentary films, and a large screen theater with realistic images of the earthquake's destructiveness.

This is an excellent museum that was built to commemorate Mount Unzen's eruptions in the 1990s and the ensuing disaster. The museum uses hands on displays and videos to educate visitors about how volcanoes work and how they affect the lives of those who live around them. The highlight of the exhibition is the eruption simulator - an immersive film accompanied by simulations of pyroclastic flow using motion and heat.

The Minamata Disease Municipal Museum documents the history of the disease with bilingual display panels, photographs and an easy to understand video presentation. It follows the current situation of the Minamata Disease and serves to remind that the tragic environmental pollution caused by methyl mercury should never happen again.

Ghibli Museum is a must-visit destination for fans of films by Miyazaki Hayao's Studio Ghibli, one of Japan's most famous animation studios. The museum exhibits the history and techniques of animation, and it has a small theater which shows short movies by Studio Ghibli that are exclusive to the museum. Many of the studio's most popular characters can be found at the museum in forms such as life-sized statues and large plush toys.

Bonsai enthusiasts should visit the Omiya Bonsai Art Museum, a superb museum which educates visitors about the various aspects of bonsai. English audio guides and well written English descriptions explain clearly how to appreciate the art form. The museum is located within the Omiya Bonsai Village, the home to multiple bonsai nurseries.

The Sand Museum exhibits large sand sculptures built by master artists from around the world. The sculptures, some several meters high, are based around a central theme that changes with each exhibition. The museum is located next to the Tottori Sand Dunes, which delivers a quasi-desert experience unique in Japan.

Fans of beer should visit the Sapporo Beer Museum, which is an attraction simply for the famous Sapporo Beer that it serves and the great beer restaurants beside it. The museum itself introduces the history of beer in Japan and the process of beer making, but has few explanations in English.

Toto has been the leading producer of toilets and washlets in Japan. Their museum next to the company headquarters in Kitakyushu, illustrates the evolution of the company and its products.