Globe-trotting gastronomy: In search of sushi perfection in Japan

'Should micro-cress not be considerably smaller than this?" I opine, staring down at the arguably macro vegetation crowning my prawn and abalone salad in a swanky Kyoto dining-room. A notionally rhetorical question which nevertheless causes my companions to bust various guts in response. With not an ounce of self-awareness intact, it seems, I've been struck down by a case of über-gastro-poncery – something it will take more than a few of my signature ketchup sandwiches back home to relieve.

Such are the perils of dining in Japan, a country where food is more venerated than Steve Jobs, restaurants are as common as streetlights and there are approximately 736 types of radish. I'm here to scratch the surface of the country's food culture on a five-day tour of Tokyo and Kyoto organised by Tetsuro Hama, the owner of Soho Japanese restaurant So. Truth be told, my experience of Japanese cuisine doesn't amount to a hill of soy beans. There's the odd, misbegotten attempt at making tempura here and the odd restorative bowl of noodles there, with lots of clammy supermarket sushi in between. Though many a Brit seems to share my gastronomic blind spot, judging by my straw poll of friends. Blame it, perhaps, on the ingrained connection between Japanese food and pocket-singeing expense thanks to your Nobus, Zumas et al.

Not that my time in Japan is parsimonious. Direct from the airport, our eating begins in earnest at Charyu Ichimatsu, a Tokyo ryotei in the downtown district of Asakusa. These exclusive restaurants are where the power elite have traditionally come to cut deals over fine food and geisha entertainment. Our presence confirms they're a tad less exclusive than that these days, though the accoutrements of exclusivity still prevail: a bucolic courtyard garden, private dining-rooms and kneeling kimono-clad waitresses, whose effusive introductory bowing leaves me spasming like a wind-up toy in return.

This bit of mis-ceremony over, we squeeze into our low table and brace ourselves for a full-on kaiseki. With its small plates and endless courses, this ancient form of haute cuisine has been credited with inspiring the global tasting-menu phenomenon. But where its Western cousin is oft-associated with fussiness, the dishes here – each representing a different cooking method – are startlingly lucid. (And oh for the crockery! Dramatically looped earthenware bowls, leaf-shaped plates with vein detailing.) My favourite? A dead heat between an aperitif of radish, apple and smoked salmon, with a sherbet-like crust of frozen rice-cake powder; and a silky, golden savoury fish custard topped with cod roe and eringi mushrooms. Though my enjoyment of the latter might have something to do with my weird, posturing enthusiasm for gelatinous textures.

Conversely, all macho pretensions are knocked out of me the next morning, as I find myself squashed against polystyrene crates for the fourth time in a matter of minutes. It's 7am, and I am at Tokyo's Tsukiji fish market, at once a must-see on the tourist trail and a place where tourists are marginally less welcome than E.coli. If you're not chastened by the forklift-truck buggies buzzing around like anarchic escapees from a Bond lair, then you will be by the scowls of the traders as you get in their way. Still, it's worth it for a selection of marine life that makes Billingsgate look as exciting as a Basildon Bond warehouse: mussels as big as chihuahuas, fish with snouts the length of aardvarks, crustaceans glowering in crates, and a spectrum of reds, from ruby sea-bream gills to wine-dark whalemeat.

Then there's the tuna. If Tsukiji is famous for anything, it's the dawn auctions where the lucrative sushi staple sells for fantastical prices – a 269kg fish recently went for a record-breaking £473,000 – and where concerns about over-fishing remain controversially off the menu. Since the auctions are closed to the public around my visit at New Year, I miss out on the high-decibel drama of the trading floor – though the squall of the industrial saws laying into the newly sold fish is aural assault enough for a morning.

We then head for a sushi breakfast at one of the tiny bars lining the outer market. Perched at an L-shaped counter, I squint to decipher the assembly process, only to be left floundering by the chef's balletic blur of hand movements. Nigiri follows nigiri, the slabs of fish meltingly fresh; the rice equally revelatory: airy, pillowy and – crucially – warm. What is this Western, sushi-desecrating hegemony that has had me chowing down on cold rolls all these years?

That evening, I meet up with the Tokyo Fixer, aka Shinji Nohara. A culinary tour-guide extraordinaire, he's shown the great and the good, among them the chef Anthony Bourdain, around his favourite hang-outs. Nohara is every bit as genial as his moniker is shadowy, though the name is in keeping with a food scene that prides itself on its sense of mystery. He estimates there to be more than 100,000 restaurants in Tokyo, with the best being "well-hidden and challenging to find for those who don't speak the language." k

"I think what makes our food culture stand out is that [people] really like to focus on one thing," he adds. And what better example of such micro-specialism than ramen? Sure, the wheat noodles originated in China, but it's the Japanese who have elevated them to obsession. Served with multifariously flavoured soups and toppings, the haute-comfort food has given rise to countless blogs, competitions and a national museum-cum-theme-park. They've even inspired a "ramen Western", 1986's comic, but not entirely absurd Tampopo, in which a man-with-no-name type comes to the aid of a sub-par, widowed chef like Clint Eastwood channelling Gordon Ramsay.

With more than 8,000 ramen places in Tokyo, the hunt for the perfect bowl is Sisyphean. Nohara takes me to one of his favourite shops, Kaduya in the Meguro suburb, whose soups he credits with the complexity of a fine wine. It is talk that you might consider not a little whimsical until you find yourself meditatively sniffing the fat-mottled surface of a bowl of their classic shoyu, or soy-based, ramen. With pork, chicken, vegetable and fish broths brewed separately, then mixed, the result is a splendiferous swirl of flavours that reveal themselves just as soon as the temperature has dropped below palate-blistering. The only downer is the chorus of rat-a-tat background slurps. The slurp may be the officially sanctioned noise of ramen appreciation, but it induces a Pavlovian shudder in this purse-lipped prude.

Early next morning, we take a paradoxically slow bullet train to Kyoto, Japan's temple-laden ancient capital. In accordance with Kyoto's status as the historic centre of Japanese Buddhism, its cuisine is known for its gentle, religiously unobjectionable seasoning and vegetarian focus. But if that sounds all too ascetically worthy, then a visit to Kanga-an quickly sets you right.

Hidden away down a nondescript backstreet, the grandiose 17th-century temple serves up fucha-ryori, a vegan cuisine originally served to monks after their ritual tea ceremonies. Twelve courses long, the menu compensates for ingredient limitations with a florid imagination and frankly ludicrous colours: there are quasi-fluorescent yellow squashes, lurid clumps of red seaweed and unidentified violet purées. There are orchid flowers fried in an egg-free tempura batter – they taste, naturally, like chicken – and mock chestnuts, consisting of sweet potato encased in spiky "husks" of noodles coloured with green tea. For a moment, you're inclined to believe there was culinary invention before Heston Blumenthal.

Lunch is burnt off with a walk up to the Kiyomizu-dera temple complex before evening comes and it's time to retreat to the hills – or more specifically Hoshinoya, a luxury twist on the traditional ryokan inn up in the mountains to the west of the city. Inside, the rooms are an inviting blend of historical romanticism and mod cons: sliding glass doors, low futon-style beds, super-sexy lighting and motion-sensor loos that unfurl themselves like a Transformer.

In keeping with this hybrid approach is Hoshinoya's on-site restaurant. Bringing French influences to bear on the traditional kaiseki, chef Ichiro Kubota's cross-cultural inspiration manifests itself in various impressive ways, from an amuse bouche of a kumquat in Grand Marnier syrup to a red carrot potage garnished with a rice cake to evoke the "image of [a] New Year's rising sun". Yet for some reason the excitement of all this artistry quickly palls. Maybe it's the ingratitude of the gastrically fatigued. Or maybe it's just that nothing could hold a candle to the next morning's discovery of a JAPANESE SCOTCH EGG. Well, that's at least how I have decided to christen the octopus-and-quails egg lollipops at the city's covered Nishiki market. If only all markets were as batty: just as memorable as the plentiful barrels of pickled vegetables are the voluminous platters of plastic "replica" sushi and a toy cat dancing to Shania Twain in the middle of a fish stall.

Back in Tokyo for our last night, there's just time for a walk on the wild-ish side. First up, I hit Omoide Yokocho, the fragrantly nicknamed "Piss Alley", a steam-swathed, post-war shanty street that remains a bastion of insalubriousness in a city of gleaming efficiency. Curling your way past refreshed clientele, you will find food shack after food shack giving it the full nose-to-tail, from forbidding pots of offal stew to hormone-yaki or grilled organ meats. I squeeze in at one cramped counter to try some chicken yakitori. A few doors down, others in the group rhapsodise over their balls of tempura vegetables in broth – no matter the broth's provenance from a mystery tap.

And then it's fugu time. For four days, I've been banging on about wanting to try the venomous blowfish, such is my puerile fascination with its lethal potential. (Fugu chefs spend years training to safely remove its poisonous parts, such as the liver and ovaries, a smidgen of which can kill in minutes.) With the rest of the group less keen, however, Mr Hama deposits me at a basement restaurant near Shinjuku station to foster my death wish alone. I order a plate of fugu sashimi, followed by some grilled sperm sacs. Eating the fish itself is like chewing expensive clingfilm, though the balls are much better: musty and palatable. Who'd have thought it? But taste is less important than an intensely in-body experience: as I quiver pathetically, every mouthful seems to squeeze its way down my gullet like a particularly un-rolling stone. I'm finally snapped out of my neuroses by two amusingly bemused fellow diners, who smell (and stare and smile at) my fear before archly informing me that I need to go to Japan's southernmost island, Kyushu, to experience "real fugu danger". Scratching the surface, did I say? I haven't even pecked it, goddamit.

Hugh travelled courtesy of So Restaurant, London W1 (020 7292 0767, sorestaurant.com). Seven nights in Tokyo with Virgin Holidays, including scheduled flights with Virgin Atlantic from London Heathrow direct to Tokyo and accommodation at the Keio Plaza Hotel Tokyo, on a room-only basis with transfers included, starts from £1,399 (virginholidays.co.uk, 0844 557 3859). For bookings and enquiries for Hoshinoya in Kyoto, visit hoshinoyakyoto.jp/en or call +81 50 3786 0066