Japan's hidden gems: where to go when Kyoto is full

Nothing in this article is a secret; it is simply not on the Tokyo, Kyoto, Osaka line that almost every visitor rides. Japan's crowding is not national, it is concentrated, and the fix is usually one transfer. Shirakawa-go proves the point: 95 percent of its visitors are day trippers, so anyone who stays the night effectively has the village. The same logic works everywhere. Arrive when the coaches leave, sleep where everyone else only stops, and eat dinner in a town whose restaurants are aimed at the people who live there. The practical cost is that English thins out fast once you leave the main cities.

Kanazawa is what people hope Kyoto will feel like. It is the capital of Ishikawa Prefecture on the Sea of Japan side, home to about 466,000 people, and in the late 17th century more than three quarters of it was samurai housing, which is why whole lanes of earthen walls survive. Kenroku-en, originally the outer garden of Kanazawa Castle, opened to the public in 1875 and is counted among the three great gardens of Japan, with ponds, waterfalls and trees over 10 hectares. Since the Hokuriku Shinkansen opened on 14 March 2015, the trip from Tokyo takes around two and a half hours. Autumn and winter are the wettest months here, so bring a coat.

Shirakawa is a village in Gifu Prefecture with about 1,630 residents, and it is on the World Heritage list for its gassho-zukuri farmhouses. The steep thatched roofs were built that way to shed the snow that buries this valley every winter. It was inscribed by UNESCO in 1995, together with Gokayama in Toyama, and tourism grew sharply from then on. The number that should shape your visit is the one in the survey: 95 percent of visitors come only for the day. Stay in one of the farmhouses that take guests and you get the early morning and the lit evening, which is the whole reason to come. Mount Hakusan, at 2,172 metres, is the high point above the village.

Nikko is the one with the shrines in the cedar forest; Hakone is the one with the hot water and the view of Fuji. Nikko sits about 140 kilometres north of Tokyo in rural Tochigi, with elevations from 200 to 2,000 metres, plenty of onsen, and the mausoleum of Tokugawa Ieyasu at Nikko Tosho-gu. There is a local saying that you should never say kekko, meaning splendid, until you have seen Nikko. It is cold up there: the annual average is around 7 degrees. Hakone is a small spa town in Kanagawa of under 11,000 people, built around Lake Ashi, the Hakone Shrine and hot springs within sight of Mount Fuji, and it is mild by comparison at around 13 degrees a year.

Ishigaki is closer to Taiwan than it is to most of Japan, and it does not feel Japanese in the way Honshu does. The island lies roughly 411 kilometres south-west of the Okinawa main island and about 300 kilometres off the north-east coast of Taiwan, and it is the transport hub of the Yaeyama group, served by New Ishigaki Airport. Much of it, including Mount Omoto and Kabira Bay, is protected inside Iriomote-Ishigaki National Park. The cooking is Okinawan, built on chanpuru, a word meaning something mixed, and it draws on Chinese, Japanese, South East Asian and American influences. Miyaradunchi, a governor's residence from around 1819, is the island's Important Cultural Property.

Trains reach four of these five; the fifth needs a flight. Kanazawa is on the Hokuriku Shinkansen from Tokyo, Nikko and Hakone are regional trains out of the capital, Shirakawa-go is reached by bus from the nearest rail town, and Ishigaki needs a domestic flight. IC cards such as Suica and Pasmo work on local trains, subways and buses nationwide, which removes most of the ticket-machine problem. Book beds well ahead for Golden Week in late April and early May, for Obon in mid-August and for New Year, when the whole country moves at once. Goodbars sells a Japan eSIM you install at home and switch on when you land; it runs on NTT docomo, Japan's largest mobile network by mobile contracts, and our Japan coverage page shows where it reaches and what independent speed tests measure.