Access all areas: a bike tour is one of the best ways to see the busy streets of Tokyo

The tour takes visitors from the smart financial district to fish markets and buzzing downtown areas. You'll even see the city's very own Eiffel Tower

Ask a Tokyoite what they'd do if they found a 10,000-yen note, and invariably you'll get the same answer: why, give it to the police, of course. Subtext: I'm shocked that you ask. Two things, however, you are in danger of having nicked. One: your umbrella. (Better to think of them as communal, and of buying a new one as a sort of community gesture.) And two: your bicycle. Add to this the ever-present danger of having your bike impounded, or of cops lurking in bushes and jumping out at you to check your registration, and it makes cycling in Tokyo somewhat stressful for neophytes.

Which is too bad, because otherwise Tokyo is paradise for bikers. First, it's flat – like many countries, Japan built its biggest metropolis on its best arable land. Second, you can ride on the pavement, and since everyone walks in predictable lanes, like shoppers at Ikea, you can weave through crowds on your mamachari basket-bike with the hellcat speed of a granny heading for the tea towels.

And third, downtown Tokyo is a veritable drip-painting of hidden temples, cheap noodle joints, tiny parks, smoky bars and ancient shops, most of which you would never find if you didn't hop on your bike first.

Yukiko Koezuka knows all this. It's why her company, Alive and Kicking, started offering the Great Tokyo Cycling Tour – an ideal way for visitors to experience Tokyo on two wheels without having to worry about theft, hedge police or any of the rest.

A charming 40-year-old who looks a decade younger, Koezuka begins her 31km tour at 9am in the shadow of the Marunouchi Hotel. This is one of a dozen high-rises that dwarf the old red-brick façade of Tokyo Station, one of the few buildings to survive the American firebombing of 10 March 1945. Against the expanses of shining steel and battalions of black taxis, Koezuka's brand-new, colour- coded hybrid bikes seem like Fisher-Price toys. And when we're strapped into our helmets and racing gloves, Marunouchi reveals itself for what it is: one giant potential BMX park. We set off and whizz off through the crowds.

Our first stop is the great Imperial Palace Road – essentially a very broad gravel driveway that links Tokyo station to the front gates of the Emperor's residence. The road was built to provide an escape route for the royal family in times of trouble – they've even got their own underground entrance to Tokyo station. We cross the palace moat via a stone bridge. The swans and joggers – and the lack of cars – make it easy to forget that we're in the centre of what may be the planet's densest urban conglomeration.

We follow Koezuka back over the moat and into the Nihombashi financial district. A line of foreigners in silly helmets on bright bikes ought to be obvious eye candy for the Japanese sararimen in their funereal suits coming in and out of the Tokyo Stock Exchange, but they're too polite – or preoccupied by the credit crisis – to stare. Pavement-biking through this buzzing district proves remarkably easy, especially in single file. Pedestrians react promptly when you ring your bell and, in true Japanese style, nobody makes any sudden moves.

After ducking under a highway overpass, Koezuka pulls us up in front of a stone wall, grass growing along the cracks: one of the six gates of Edo (the name for Tokyo before it became the capital). Built to defend the city in a pre-nuclear world, it's now ignored by the surrounding hive of Japanese finance that has grown to be a much more modern – and effective – line of defence. Only a tiny plaque commemorates the gate's old purpose.

After a brief rest, we're off down a series of tiny side streets, lined with clipped hedges, over an ancient wooden bridge – and back several centuries into the past. Tsukuda-jima is a tiny island, inaccessible by public transit, ignored by tourists. Gnarled trees curl around the wooden houses, some of which are hundreds of years old – the equivalent of pre-Cambrian in Tokyo terms.

Here, the shogun Tokugawa Ieyasu granted a lucrative favour to the tiny village of Tsukuda, whose residents helped him cross a river 30 years before: a parcel of land and exclusive fishing rights along Edo's shore. Thirty-three families took him up on the offer. Edo sprung up around them – the first beginnings of the concentration of wealth the city now represents – and their descendants still live here, in the shadow of the financial high-rises.

On one quiet street, under fluttering laundry, master chopstick-carver Nakajima-san straddles a bench, patiently whittling. His shop has sold laquerware and other traditional goods for over 300 years. Steadfastly ignoring our cameras, he stacks his finished chopsticks into a box marked Amazon.com.

Further down is one of three shops here that sell tsukudani, the area's famous foodstuff: boiled, salty-sweet fish gelatin that the fishermen would make to preserve their catch. Koezuka whips out a clear plastic bag: tsukudani, warm and squishy.

Nearby, on the muddy river under the Tsukudakobashi bridge, ancient barges are moored to rickety wooden piers and tended by men in yukata and headbands. We head down a tiny unmarked alley – and between the buildings come across a tiny shrine, built around a huge tree. A praying woman turns around angrily at our camera flash. Koezuka hurries us out to the Sumiyoshi Shrine, where people still pray for safety before they head out to sea. The 33 fishermen are commemorated in wooden carvings above the prayer fountain, where we clean our hands using a long bamboo ladle. Near a glaringly white wooden pole reading "May Peace Prevail on Earth", someone has parked a gangster-sized Mitsubishi scooter.

Of course, the seafood industry in Tokyo has expanded somewhat beyond 33 men. A short bike ride away and we're suddenly swerving around hook-wielding fishermen driving motorised flatbeds loaded with tuna, fresh from the 6am auction. This city-within-a-city is Tsukiji Fish Market, an endless warren of dripping Styrofoam stalls occupied by bare-chested men sawing off metre-long marlin tusks and laughing at tourists, all housed under a sprawling open roof that curves away out of sight. It is a glorious anachronism – and one that the indebted Tokyo municipal government, blind to its magic and hungry for its real estate, is planning to shut down and relocate.

Koezuka forgoes the bento-box lunch she normally provides and instead takes us to Sushi Dai, widely considered the best sushi joint in Tsukiji – and thus probably the world. The sashimi here was in the sea two hours before: some of the fish is still electrically sensitive and snaps into a curl when the head chef flicks it; the chu-toro (fatty cut of tuna), closer to butter than seafood, will ruin lesser-quality sushi for you forever.

Stuffed but surprisingly full of energy, we start off in the direction of the new fish market location – which means biking across Tokyo Bay. This is the only part of the tour that can be considered a slog, though the second half is an easy coast down to Odaiba, a massive chunk of reclaimed land plopped down in the middle of Tokyo Bay.

It doesn't make for particularly beautiful cycling at first: the new site for the fish market is still just a weed-covered field. In the middle stands the huge blue Lego piece that is Shijo-Mae monorail station, which will eventually be the main stop for the market; for now it is a deserted hulk. After a few minutes, a monstrous shopping and entertainment complex comes into view. Here lies Japan's largest Ferris wheel, an artificial beach (swimming discouraged), a half-sized Statue of Liberty, and herds of cooing young couples.

But the surrounding area turns out to be surprisingly pretty when you bike through it – and Koezuka knows some of the prettiest places.

After circling the island, we arrive at Hinode Pier, where a cool spaceship-hoverboat thing zooms us back across sparkling Tokyo Bay. Koezuka points out landmarks, such as Rainbow Bridge, and the old cannon batteries that once tried in vain to defend Tokyo from Commodore Perry's Black Ships. These four US steamships easily brought pre-industrial Japan to its knees in 1853, forcibly ending the archipelago's self-imposed 200-year isolation.

Back on the mainland, it's a short ride to Tokyo Tower, a dead ringer for the Eiffel Tower (but 13 metres higher!) that does nothing to dispel the vaguely Vegas vibe we still feel from our tour of Odaiba. We don't bother stopping, and proceed to nearby Zozoji, the family temple of the legendary Tokugawa family. It's largely obscured by scaffolding, so Koezuka leads us to a gang of stone children, each wearing little red knitted hats decorated with pinwheels and flowers. Each represents a stillborn baby; apparently, mothers can rent the stone figures to honour their little ones.

Our last stop is back at the Imperial Palace. By the time we get there, the gates are closed. The police officers in the guard booth look at us warily, but after a few polite words from Koezuka they smilingly agree to pose for pictures. For once, they don't ask to check our registration.

Getting there

Direct flights are offered between Heathrow and Tokyo Narita by BA (0844 493 0787; ba.com ), Virgin (0844 874 7747; virgin-atlantic.com ), ANA (0870 837 8811; ana.co.jp ) and Japan Airlines (020-7618 3224; uk.jal.com/en ).

To reduce the impact on the environment, buy an "offset" through Abta's Reduce my Footprint initiative (020-3117 0500; www.reducemyfootprint.travel ).

Getting around

Tokyo Great Cycling Tour, 3-4-3 Shinbashi, Minato-ku, Tokyo 105-0004 (00 81 3 4590 2995; tokyocycling.jp ).

Tours run every Saturday and Sunday starting at 9.30am and the cost of Y10,000 (£63.40) includes tax, bike rental, lunch box, insurance and a guide.

On weekdays between 21 July-4 September, TGCT operates a three-hour morning ride starting at 5.30am and an evening one at 6.30pm; the cost is Y3,000 (£19), not including lunch.

Staying there

Marunouchi Hotel, 1-6-3 Marunouchi, Chiyoda-ku, Tokyo (00 81 3 3217 1111; marunouchi-hotel.co.jp ). Doubles start at Y31,385 (£199), room only

More information

Japan National Tourism Organisation: 020-7398 5678; seejapan.co.uk