One of the highlights of travelling in Japan is the chance to experience the traditional hospitality of a ryokan, such as Gora Kadan in Hakone. These quintessentially Japanese inns have no real equivalent in the West, their old-world atmosphere being little changed since the Edo period of the 16th century. Shōji sliding doors of translucent handmade washi paper, low tables and fragrant tatami mats set the tone. For dinner, guests are encouraged to don the full-length yukata and obi sashes. In Hakone, Gora Kadan boasts stone and cypress-wood hot tubs in the garden, fed by natural hot springs, from which you can gaze across the tree tops to Mount Fuji – the ultimate honeymoon view.

At the head of the ropeway overlooking Lake Ashi, the Narukawa Art Museum is definitely worth the detour – not merely for the stupendous views over the surrounding peaks from its Panorama Lounge, but the impressive collection of modern Nihonga art by Japanese masters. ‘Nihonga’ are works made in accordance with ancient Japanese principals, using traditional techniques and materials, such as washi paper and silk. Some of the finest examples ever produced are housed in this museum, and they’re as sublime, subtle and definitively Japanese as the scenery.

Rising from Kanto Plain to the West of Tokyo, Mount Fuji is Japan’s iconic sacred mountain – an active volcano whose elegantly sloping flanks have inspired painters, printers, poets and Shinto mystics for many centuries. A well-known saying asserts that it’s unlucky to climb the peak twice, but a huge number of outdoors enthusiasts and pilgrims make the ascent each summer in July and August, when the summit is ice-free and easily accessible to anyone with sufficient stamina. Less adventurous souls can admire its beautiful shape from the shores of the five lakes lapping the mountain’s base.

For a first foray in Kyoto, we suggest the trip up to the Fushimi Inari shrine on a hillside overlooking the city, where lines of inscribed, red-lacquer archways form beautiful covered walkways – one of the most romantic spots in the region. Back in the city later, stroll along the Philosopher’s Walk, a pleasant waterfront path lined with cherry trees, before dinner at Tako Nyudo, which specializes in Kyoto’s home-style of cooking, known as ‘obanzai’. Try the more-ish house speciality, ‘akashi yaki’ – pieces of delicately flavoured octopus fried in crispy egg batter.

Kyoto is the Japan of the imagination – a city of cherry trees, pagoda-roofed temples, geishas and tea ceremonies, all set against a backdrop of lush green hills and fine traditional architecture. An unparalleled wealth of period buildings survive here, from Edo-era wood-fronted houses to glittering medieval shrines crammed with sumptuous art. You’ll also have the opportunity to experience the art forms associated with them, from Japanese flower arrangement to rock gardening and the arcane costumes of Noh drama – all in their traditional contexts. And of course, there’s Kyoto’s sumptuous ‘kaiseki’ – the epitome of Japan’s über-refined cuisine.

Nara ranks among the most charismatic cities in Asia, thanks to its extraordinary collection of antique buildings, many of which are more than a thousand years old. Its UNESCO-listed centrepiece is the spectacular Todai-ji Temple, home to a 500-tonne, 16-metre-tall, bronze-cast Daibutsu Buddha. The world’s largest wooden building, the shrine now resides in a leafy park where sacred sika deer roam free, scrounging rice crackers off visitors (in exchange for which they bow their heads in true Japanese style!). The nearby museum holds a hoard of precious antiquities from the 7th century Shōsōin Treasury, a selection of which are exhibited for just a fortnight each autumn.

The wildest and most remote place in Japan, Iriomote in the Yaeyama archipelago is an island of dark green cliffs plunging to dazzling green-blue seas. As the most southerly of the Okinawas, it is a landmass so far flung that only a trickle of intrepid travellers get to enjoy its pristine, white-sand beaches and beautiful waterfalls each year. Over 90% of the island is covered in forest, so to see its hidden beauty spots you generally have to take to the water in a kayak – though when you’ve seen it, you may find it hard to tear yourself away from your luxurious tropical hideaway, the Hotel Nirakanai Iriomotejima.

An easy half-hour walk from your hotel, Hoshizuna is famous in Japan for its star sand. The five-pointed grains are not technically sand, but the exo-skeletons of tiny, one-celled organisms called Foraminifera that live among the sea grass off shore. This is one of only two places in the world where such a phenomenon occurs and it creates a special atmosphere. The water at Hoshizuna is the trademark shimmering, transparent turquoise of the Okinawas, and a great place for swimming and snorkelling. Spend the remainder of the day kayaking up the mangrove-lined Mizuochi River to a beautiful waterfall. Return for a candle-lit supper for two on your private verandah.

Taketomi exists in a delightful time warp. Only 351 permanent residents live on it, most of them in a huddle of red red-tiled, one-story houses encircled by pretty white coral walls (curved, it is said, to deter local demons, who only walk in straight lines!). You’ll find the same low stone walls surrounding your cedar-built villa, which is furnished with fragrant tatami mats and shoji screens. A grassy path leads to the nearest beach, only a stone’s throw away, and there’s a gorgeous pool, carefully tucked away but with an expansive view.

A dazzling spread of shallow turquoise water greets your arrival at Kondoi. Despite appearing regularly in roundup pieces on the ‘World’s Most Beautiful Beaches’ it sees relatively few visitors and is remains low-key even at the height of season, with just a scattering of parasols and single changing room to break up the exquisite expanse of gleaming, powder soft shell sand. Offshore, a scattering of seven islands are dotted over an unfeasibly blue sea. Kondoi is reachable on foot from your hotel, or you can get there on a rented cycle or by bullock cart – the much loved ‘Taketomi Taxi’!

It’s worth setting aside a day to visit north coast of Ishigaki to see the beautiful turquoise water and limestone islets of Kabira Bay, where you can swim over reefs swirling with yellow-lipped triggerfish. Glass-bottomed excursion boats run out to nearby Manta Point, a superb dive site where rays congregate in numbers. For total wilderness, you could also continue on by local bus to deserted Yonehara Beach, which many rate as the loveliest in the Okinawas. Back at Hoshinoya, enjoy the mouthwatering fusion cuisine whipped up in the resort’s restaurant: we recommend the grouper sashimi with shredded carrot salad and sea grapes, rounded off with a heavenly tofu tiramisu.

A great source of quirky Japanese souvenirs in Tokyo is Oriental Bazaar, at 5-9-13 Jingumae, in Shibuya. It’s the most famous gift store in the capital, offering a wide choice of dolls, kimonos, yukata, curios and books. The staff speak English and the prices are restrained. Afterwards, head for the Tokyo Skytree in Ashiage, officially the world’s highest broadcast tower: the views over the city from the glass-floored Sorakara Point extend to Mount Fuji – a suitably stellar view with which to end to your trip.