Kanda Yabu Soba

In a city that has celebrated the understated flavour of soba (buckwheat noodles) for centuries, no restaurant is as revered as Kanda Yabu Soba. Founded more than 100 years ago, it's a handsome, free-standing wooden villa in its own tranquil garden courtyard with the feel of a traditional tea house. Kimono-clad waitresses bustle about, ferrying food and drink from kitchen to table (either with chairs or on tatami mats). Locals prefer their noodles cold, as zaru soba (plain noodles with a dip) or ten-zaru (the same with batter-fried shrimp). In winter the classic dish is kamo-nanban, hot soba in a rich broth with slices of duck breast and leek.
• 2-10 Kanda-Awajicho, Chiyoda-ku, +81 3 3251 0287, norenkai.net/english/shop/yabusoba/index.html, soba noodles from around £6. Open daily 11.30am-8pm. English menu

Tsunahachi Rin

Tempura – batter-fried morsels of seafood and vegetables – is one of the supreme delicacies of Japanese cuisine and, like sushi, at the upper end it can cost a prince's ransom. Hidden away on the upper restaurant floor of a mall close to Shinjuku JR Station, Tsunahachi Rin proves it doesn't have to. Drawing a youngish demographic, it brings some innovative nuances to the tradition, such as serving a choice of four different kinds of salt with the tempura instead of just the standard soya-based dipping sauce. Drop in for a quick, affordable lunch of tendon (shrimp and a few cuts of vegetables served on rice), or settle in for a leisurely dinner, picking from the considerable side menu of sashimi and other Japanese delicacies.
• Lumine 7F, 3-38-1 Shinjuku, Shinjuku-ku, +81 3 3352 1012, tunahachi.co.jp, lunch from ¥1,260 (£10.50), dinner from ¥2,625 (£22), English menu. Open daily 11am-11pm

Sushi-Bun

Tokyo's central fish market is an essential part of most visitors' itineraries, and so is breakfast at one of its legendary hole-in-the-wall sushi counters. The seafood could hardly be fresher, and the sushi is as good as you'd expect at places charging four times as much. Sushi-Bun is one of the best in the market – it's just as tiny (10 seats at the counter at a pinch) and as tasty as the others, but it's left out of most guidebooks so the queues are usually shorter. Most people go for the set sushi menu (from £22 for eight servings of whatever seafood is in season, plus soup), which includes their succulent house-special, anago sea eel. The rough sake they serve with it, though, is far from premium.
• 8 Chuo Shijo Building, 5-2-1 Tsukiji, Chuo-ku, +81 3 3541 3860, tsukijinet.com, sushi chef's menu (omakase) from £22, English menu. Open Mon-Sat 6am-2.30pm, closed Sun and holidays

Kushiwakamaru

Yakitori – bite-sized cuts of chicken (and some vegetables) skewered, grilled and then seasoned with salt or slathered with thick soy sauce – is classic blue-collar fare: cheerful, affordable and best washed down with flagons of lager, sake or shochu. The cheapest places tend to be raucous and smoky, and often specialise in offal, but Kushiwakamaru hits just the right note. The feel is casual and accessible, while the charcoal-grilled chicken is well above average. There are always a few specials, such as duck or quail. And don't miss the negima (chicken and leek), the tsukune (balls of minced chicken) or the tebasaki chicken wings (forget chopsticks – these you pick up and gnaw with your hands).
• 1-19-2 Kami-Meguro, Meguro-ku, +81 3 3715 9292, r.tabelog.com/tokyo/A1317/A131701/13003193, yakitori from £1.60/stick, English menu. Open Mon-Fri 5.30pm-midnight, Sat-Sun 5pm-midnight

Nogizaka Uoshin

Five minutes' walk from the opulent Roppongi midtown complex, the Nogizaka branch of the Uoshin group sets the template for the genre that's come to be known as fish shack dining. Fresh seafood served any which way you like, at prices that reflect the rudimentary decor: bright lights, colourful fishermen's banners and no-frills seating. Uoshin's parent company is a seafood wholesaler, guaranteeing freshness and a great variety of seasonal seafood. You can't go wrong here: generous sashimi platters; whole squid or other fish grilled to order; warming winter fish stews; and humongous portions of sushi.
• 9-6-32 Akasaka, Minato-ku, +81 3 3405 0411, uoshins.com, full meals from around £30, including two hours of all you can drink. Open Lunch 12-2pm on weekdays; dinner 5pm-12am; Sunday and holidays 4pm-11pm

Maruni

Maruni does barbecue in a style all its own. The building is an old converted rice merchant's store that somehow got left behind among the modern office buildings close to Shinbashi Station. The decor is all gaudy black and red. Instead of tables and chairs, there are half a dozen oil drums, each with a charcoal grill set into the top. You just order a plate or two of meat, then grill it yourself. The beef is all from the famously pampered Japanese wagyu cattle. Maruni doesn't serve the super-premium steak grades so it's all highly affordable.
• 1-11-1 Shinbashi, Minato-ku, +81 3 3572 1129, r.gnavi.co.jp, grilled beef from around ¥550 (£4.60 a plate. Open Mon-Thurs, Sat 5pm-midnight, Fri 5pm-4am. English menu

Ippudo

Ramen is Chinese in origin, but it's unquestionably Japan's de facto favourite late-night fast food. You find ramen counters on virtually every street corner, serving up nourishing, steaming hot bowls of wheat noodles in rich, meaty broth, invariably topped with slices of chashu pork, half a boiled egg and chewy strips of menma bamboo. Within the genre, though, numerous regional variations have evolved: all are available in Tokyo. Where to start? You can't go wrong with Ippudo, a chain (now with a New York outlet) that flies the flag for Fukuoka ramen. The noodles are light and the tonkotsu soup (made from long-simmered pork bones) rich and satisfying.
• 1-3-13 Hiroo, Shibuya-ku, +81 3 5420 2225, ippudo.com/store/tokyo/ebisu.html. Open Mon-Sat 11am-4am, Sun 11am-2am. English menu

Shin-Hinomoto

There's nothing in the West quite the equivalent of an izakaya: neither pub nor restaurant, it's a place for eating — often well and always cheaply — as much as for drinking; and, just as importantly, for de-stressing after work. Shin-Hinomoto is a classic example. It looks unpromising, a cramped room full of noise and cigarette smoke shoehorned in under the railway tracks in Yurakucho. It's a typical izakaya in all but one respect: the master of the house is British. Known to one and all simply as Andy, he married into the business and now runs it. Seafood is his speciality, which he sources each day from Tsukiji market. But you'll also find chicken, cooked vegetables and simple salads alongside the tempura and sashimi.
• 2-4-4 Yurakucho, Chiyoda-ku, +81 3 3214 8021, andysfish.com/Shin-Hinomoto. Open Mon-Sat 5pm-midnight, English spoken

Little Okinawa

The food and drink of Japan's southernmost prefecture are so distinctive they could be a totally different cuisine. The Okinawa archipelago is far closer to China than to Tokyo and the influences are marked. Little Okinawa is a welcoming, long-time (yes, and very compact) bastion of this subtropical culture, and it serves all the island exotica. Start with umi-budo, seaweed resembling miniature grapes, and jimami-dofu, a tofu-like custard made from peanuts. Continue with goat sashimi and pig's ear (crunchy, but served with a nice vinegar-sharp sauce). And don't miss the goya-champur (scrambled egg, tofu and bitter gourd) and rafutei, pork belly soft-simmered till you can cut it with a chopstick. Wash it all down with shots of awamori, a fiery liquor that can pack a wallop.
• 8-7-10 Ginza, Chuo-ku, +81 3 3572 2930, little-okinawa.co.jp, starters from £4.50; stir-fries from £7; noodles from £6.50. English menu. Open noon-1.30pm, 5pm-3am Mon-Fri, noon-1.30pm, 4pm-midnight Sat and Sun

Tonki

The first thing you notice about Tonki is how bright it is: it's as spick and span as an operating theatre. The chefs wear spotless white uniforms, the kitchen gleams and the wooden counter and tables are scrubbed smooth. Quite remarkable for a place where the only form of cooking is deep-frying. Tonki's speciality (in fact the only thing it serves) is tonkatsu: cutlets of pork that are dipped in breadcrumbs, then fried till the outside is a crispy golden-brown and the meat inside perfectly tender and juicy. You have two basic choices: rosu (blubbery-rich belly meat) or hire (lean loin "fillet"), though the latter is also offered as kushi, bite-sized cuts cooked on skewers. Most people order the set meal, with rice and miso soup on the side, leaving as soon as they finish.
• 1-1-2 Shimo-Meguro, Meguro-ku, +81 3 3491 9928, tonkatsu from £7, set meals from £14. Open 4pm-10.45pm, closed Tues and third Mon of the month

For more information go to the Japan National Tourism Organisation's website: jnto.go.jp/eng

• Robbie Swinnerton writes the Tokyo Food File column for The Japan Times