3 Best Sights in Nagoya, Ise-Shima, and the Kii Peninsula, Japan

These shrines are rebuilt every 20 years, in accordance with Shinto tradition. To begin a new generational cycle, exact replicas of the previous halls are erected with new wood, using the same centuries-old methods, on adjacent sites. The old buildings are then dismantled. The main halls you see now—the 62nd set—were completed in 2013 at an estimated cost of more than ¥5.5 billion. For the Japanese, importance is found in the form of the buildings; the vintage of the materials is of little concern. You cannot enter any of the buildings, but the tantalizing glimpses of the main halls that you catch while walking the grounds add to the mystique of the site. Both Grand Shrines exhibit a natural harmony that the more-contrived buildings in later Japanese architecture do not.

Deep in a park of ancient Japanese cedars, Geku, dating from AD 477, is dedicated to Toyouke Omikami, goddess of agriculture. Its buildings are simple, predating the 6th-century Chinese and Korean influence. It's made from unpainted hinoki (cypress), with a closely cropped thatched roof. You can see very little of the exterior of Geku—only its roof and glimpses of its walls—and none of the interior. Four fences surround the shrine, and only the Imperial Family and their envoys may enter. Geku is a five-minute walk southwest of Ise-Shi Station or a 10-minute walk west of Uji-Yamada Station.

The even more venerated Naiku is 6 km (4 miles) southeast of Geku. Naiku is said to be where the Yata-no-Kagami (Sacred Mirror) is kept, one of the three sacred treasures of the imperial regalia. The shrine, reputed to date from 4 BC, also houses the spirit of the sun goddess Amaterasu, who Japanese mythology says was born of the left eye of Izanagi, one of the first two gods to inhabit the earth. According to legend, Amaterasu was the great-great-grandmother of the first mortal emperor of Japan, Jimmu. Thus, she is revered as the country's ancestral goddess-mother and guardian deity. The Inner Shrine's architecture is simple. If you did not know its origin, you might call it classically modern. The use of unpainted cypress causes Naiku to blend into the ancient forest encircling it. To get to Naiku, take Bus 51 or 55 from Uji-Yamada Station or in front of Geku to the Naiku-mae bus stop, which is right in front of the shrine. The ride takes about 20 minutes and costs ¥440.

Considered one of Japan's best museums, Meiji-mura has more than 60 buildings originally constructed during the Meiji era (1868–1912), when Japan ended its policy of isolationism and swiftly industrialized. The best way to experience the exhibits is to wander about, stopping at things that catch your eye. There's an English pamphlet to help guide you. If you get tired of walking, hop on a tram originally from Kyoto, a steam train from Yokohama, and an old village bus; a single pass gives you access to all three for an additional fee. Among the exhibits are a surprisingly beautiful octagonal wood prison from Kanazawa, a Kabuki theater from Osaka that hosts occasional performances, and the former homes of renowned writers Soseki Natsume and Lafcadio Hearn. The lobby of legendary American architect Frank Lloyd Wright's Imperial Hotel, where Charlie Chaplin and Marilyn Monroe were once guests, is arguably the highlight. It opened on the day of the Great Kanto Earthquake in 1923, 11 years after the death of Emperor Meiji, and though it is not strictly a Meiji-era building, its sense of grandeur and history are truly unique. Buses run from Inuyama Station to Meiji-mura two to three times an hour from 9 to 4. The ride takes 20 minutes and costs ¥430.

If time is limited, head for this memorial park first. Many Japanese make pilgrimages to the mausoleum of Kobo Daishi or pay their respects to their ancestors buried here. Arrive early in the morning, before the groups take over, or even better, at dusk, when it gets wonderfully spooky.

Exploring this cemetery is like peeking into a lost and mysterious realm. Incense hangs in the air, and you can almost feel the millions of prayers said here clinging to the gnarled branches of 300-year-old cedar trees reaching into the sky. The old-growth forest is a rarity in Japan, and among the trees are buried some of the country's most prominent families, their graves marked by mossy pagodas and red-robed bodhisattvas.

You can reach Okuno-in by way of the 2½-km (1½-mile) main walkway, which is lined with more than 100,000 tombs, monuments, and statues. The lane enters the cemetery at Ichi-no-hashi-guchi; follow the main street straight east from the town center for 15 minutes to find this small bridge at the edge of the forest.

The path from Okuno-in-mae ends at the refined Toro-do (Lantern Hall), named after its 11,000 lanterns. Two fires burn in this hall; one has reportedly been alight since 1016, the other since 1088. Behind the hall is the mausoleum of Kobo Daishi. The hall and the mausoleum altar are extremely beautiful, with subtle lighting and soft gold coloring.