Two hours from the neon of Tokyo, Liz Boulter meets a family with a back-to-nature outlook who run an inn on a farm that pays its dues to Japan's ancient traditions

Yosuke removed the gauze from the giant bucket to reveal a seething brown mass. "This is our own shoyu," he said. "Soya beans, wheat, salt, water and koji bacteria sit there for four months, then it's pressed and fermented again. We make over 50 litres every year."

To one used to soy sauce in neat little bottles, the bubbling goo looked far from appetising, but doing things the neat, convenient way is not what Brown's Field farm – and its latest addition, an inn called Jiji's – is about.

We were a couple of hours from Tokyo on the Boso peninsula: the view from the train started with a succession of dull dormitory towns, but suddenly switched to green knobbly hills and flat rice fields.

Yosuke's parents-in-law, US-born photojournalist Everett Kennedy Brown and his wife Deco Nakajima, a teacher of macrobiotic cooking, moved here 15 years ago, tired of living in Tokyo with their five children. They bought the two-acre farm and set about shaking off their urban selves, farming sustainably and organically, drawing on centuries of rural Japanese wisdom. This is a well-trodden path in Europe or America but, driving us in his biodiesel car from nearby Chojamachi station, Everett told me that here it's unusual. In Japan, few would choose simple and natural over modern and hi-tech, he said.

Their city friends still think they are mad, but several of them enjoyed coming to stay, and eventually the idea was born of opening a guesthouse.

On a bright, breezy afternoon, a young family from Tokyo were playing ball in front of one of the two guest cottages in the field in front of the farmhouse. Visitors can also stay in one of four rough-and-ready but appealing treehouses connected by Ewok-style wooden walkways. We wandered with Yosuke and his baby daughter among bamboo groves, vegetable plots and rice paddies in which dozens of white ducks waddled contentedly. It's called aigamo nohou, duck-farming, Everett later told us. "The ducks eat weeds (they can't reach the rice seedlings), their droppings act as fertiliser, and their paddling feet work it into the soil." Across the paddy, the ducks' house looks like a New England clapboard church, a nod to Everett's US east coast upbringing.

So far, so delightful. Then Yosuke showed us the toilets, which are of the composting variety. You wash your hands in harvested rainwater, using only in the biodegradable toiletries provided. Bedrooms are bare and functional, futons and duvets rolled in one corner. Chickens, dogs and interns (students and Wwoofing volunteers) were busy around the ramshackle-looking main farmhouse. Macrobiotic meals are eaten communally – family, staff, volunteers and guests elbow to elbow at a long table.

Tree house accommodation at Brown's Field. Photograph: Tony McNicol

But what about comfort? What if you prefer contemporary to basic? With such visitors in mind, Everett bought a big old house a short walk from Brown's Field, and opened it last year as a six-bedroom "country inn". Its name, Jiji no Ie, means "grandpa's house", though this would have been a very sophisticated grandfather. Five of the rooms are Japanese in style, with beautiful organic tatami on the floors, bright cushions at low tables, exquisite carving round the doors and futons hidden inside hand-painted cupboards. (A sixth room has a western bed, with billowing drapes.) There are sliding paper screens between the rooms and the corridor, a dining room with built-in woodburner, normal flushing loos and a garden bathhouse.

Everett, who has long silver hair, and a wise manner, told us how he sought out sustainable architects and designers to make the house from local timber, earth, bamboo and straw. (This baffled the local planning authorities, who – typically, said Everett – couldn't see why he eschewed factory-made materials.) In one corner of Jiji's garden is a suikinkitsu, or water harp, a feature dating from Japan's Edo era (1603-1867) – a large ceramic jar buried upside-down in the earth. Water overflowing from a stone basin trickles through the hole in its base and makes a surprising ringing sound – the unpredictability of the drops forming sweet natural music.

Rooms at Jiji no Ie

Inside, Deco, who is as tiny as her smile is huge, was preparing dinner. Meals at Jiji no Ie are mostly vegan, but with some local cheese and fish. After an aperitif of plum wine, we sat at a long, polished table made from a single length of tree trunk for an exquisite 10-course tasting menu that included homegrown red rice crisps with hummus; carrot tempura with leek flowers; a brown rice and walnut timbale with turmeric, tomato, seaweed and pumpkin seeds; and cabbage leaves stuffed with millet and cashew nuts. Macrobiotic isn't scary, said Deco, it's just a balanced diet of natural ingredients, eaten in season, with traditional fermented foods such as tofu with koji (which gives the curd a cheesy tastiness). Fermentation, she told us, produces probiotics that help us absorb more nutrients. We drank unfiltered sake made by a friend of theirs – chock-full of good yeasts and enzymes, they assured me. Can't go wrong then, I said, accepting a refill.

We'd been introduced to Everett by Bristol-based Inside Japan Tours, which now recommends Jiji's for a relaxing few days at the beginning or end of a trip (it's less than an hour from Narita airport). After frenetic Tokyo, we relished the laid-back vibe of Chiba province, and there is plenty to fill a couple of days: cycling wooded hills; surfing at long, uncrowded Kujukuri beach; or taking tea at a 1,200-year-old Buddhist monastery.

Deco Nakajima and Everett Kennedy Brown. Photograph: Tony McNicol

You can help out at the farm – digging, milking goats, planting rice in spring – but we left that to gnarlier types. Jiji's offers less hardcore visitors a glimpse of the rustic and traditional, exquisite surroundings – and a deeper appreciation of the intense umami notes in a delicious shoyu sauce.

• Accommodation was provided by Brown's Field (brownsfield-jp.com), which charges £87pp half-board. Inside Japan Tours (0117 370 9751, insidejapantours.com) offers a week's trip from £684pp, including three nights' B&B in Tokyo, city tour, three nights' half-board at Brown's Field and airport transfers

More back to nature stays in rural Japan

Ninety minutes by train from Kyoto, the old imperial capital of Japan, lies the mountain town of Ayabe, known for fireflies and hot springs. Ayabe Yoshimizu is a thatched farmhouse guesthouse with six rooms (one a western-style twin) and two traditional bathhouses in a wooded valley.

• yoshimizu.com/english/ayabe, from ¥13,000, around £76, for two full-board

Five hours by fast train from Tokyo, Aomori prefecture in Honshu has recently started promoting farmstays. The area is known for apples, garlic, Chinese yam and tomatoes; guests here help out on the farm and spend a few days in a local farm house, eating with the family.

• greentourism-aomori.jp/en/green_tourism1.html, doubles £79 full board

In the Japanese Alps, east of Tokyo, you can rent a minka, or mountain home. These are traditional farmhouses in a style unique to this Hida Takayama region, with modern kitchens but futons and traditional fireplaces. Take guided bike tours through villages and farmlands, and visit local festivals.

• satoyama-experience.com, £88 a day self-catering

Traditional Gassho-zukuri houses in the village of Shirakawa-go. Photograph: Alamy

In the Hakusan national park is Shirakawa-go, a Unesco-listed area of tiny mountain hamlets. The traditional building style is called gassho-zukuri, or praying hands, a reference to the inverted V of the thatched roofs, pictured right, designed to cope with heavy snow in winter. Shirakawa-go can be visited on a day trip from Tokyo, but some of the buildings have been made into guesthouses, and you get a much better feel for the culture with an overnight stay. It's not luxurious, and the bathouse is communal, but you dine on traditional food cooked over the firepit.

• japaneseguesthouses.com/ryokan-single, from £41pp a night