And here's the first shock: in 1922, the waterfront was a seething maze of narrow, unpaved streets lined with market stalls aswirl with everything from vegetables to jewellery. Open sewers ran down the gutters; locals in wooden-soled sandals, women with babies strapped to their backs sidestepped rickshaws, bullock-carts and horse-drawn wagons.

Today, a huge land-reclamation programme has pushed back the sea and changed the shape of the bay. All around me are public gardens, a park with a picturesque canal. Families with children wander the immaculate paths. Not a speck of litter to be seen.

For 200 years Nagasaki was Japan's window on the world, the only port open to foreigners after their missionaries and traders were expelled. Mistrust lay at the heart of the isolation, particularly of missionaries with their agenda of conversion. The Portuguese had been there from the town's very beginnings, bringing culinary influences as well as Christianity. The Dutch were allowed to stay, but confined to Dejima, a man-made island in the bay. The island of confinement is now a museum, the wharf it faces lined with restaurants. At crowded café tables, visitors linger over a cappuccino or a sushi snack.

At every street corner signs point to Thomas Glover's Garden. The Scotsman is something of a hero here: he brought the railway to Nagasaki, built up the Mitsubishi steel works and created a dazzling garden full of brazenly colourful flowers – very un-Japanese.

Puccini's Cho-Cho didn't give much thought to horticulture, but "my" Cho-Cho, awaiting Pinkerton's return "one fine day", asks the kindly American vice-consul to advise her on flowers to please her American husband. He takes her to the Glover Garden. And here again there's a mismatch between the past and present: in 1922 visitors to Glover's palatial house came by rickshaw or horse-drawn carriage. Locals would have trudged up on foot. Today's pampered tourists glide to the top on sleek escalators and moving walkways.

The cluster of elegant European houses that survived have been formed into a lucrative, visitor-friendly complex.

Thomas Glover married a Japanese woman, and as a nudge to the visitor that this might have inspired Puccini, there's a statue of Madame Butterfly in the garden, and nearby, of the composer himself.

At first I can't find Butterfly, but suddenly, there she is: graceful in her kimono, a protective hand on the shoulder of the child she will despairingly hand over to his American father. The statue is a bit kitsch and strains of a lush Puccini soundtrack drifting through an open door from a video suggest it's time to move on, to reality.

Like San Francisco, which suffered destruction of a different sort, Nagasaki is very much a modern city; high-rise blocks, traffic systems. The old world ended on August 2 1945 when, at 11.02am, an atom bomb fell out of the sky and blasted the town and its people to what could have been oblivion. Instead, it proved a horrific moment of rebirth. The people of Nagasaki overcame that day of devastation to build a living, bustling town that refuses to be defined by the bomb; a vibrant city. But there are reminders: the shattered stone Torii gate looming at the top of a flight of steps; the Peace Park, the place that marks the detonation, with widening rings drawn on the ground from the epicentre of the blast.

A visit to a museum commemorating death and destruction would not normally figure on a must-see tourist list, but the Nagasaki Atomic Bomb Museum transcends categorisation. An extraordinary building, it's something of a Tardis: small on the outside, drawing you into a dark universe. A shallow ramp steers you in a widening spiral down into a shadow world lit up with vivid fragments of nightmare; videos, pictures, interactive displays, survivor testimonies; the horrors faced with quiet dignity and clarity. Terrible, yes, but cathartic. The end of the story is survival of the human spirit.

Due to Nagasaki's geographical formation, some precious buildings survived the explosion. Traditional wooden dwellings disappeared, but the charming 17th-century double-arched stone bridge affectionately known as the Spectacles still spans the Nakajima river. The Oura Catholic church also withstood the blast, as did Tera-machi – Temple Row – a complex of calm and beautiful grey stone structures, linked by gardens, that includes the oldest Obaku Zen temple in Japan.

I criss-cross the town from waterfront to upper hillside, finding remnants of the past at every corner: Hollander Slope, lined with the houses where Europeans lived - unexpectedly grand, wider than other old streets because it was used for horse-drawn carriages. In the poorer districts goods were transported on foot or rickshaw. Higher up the hill is the site of an old looking post for observing those suspicious foreign ships entering and leaving the harbour.

To get a view of the town from the water you can take a cruise around the bay. Or float to the top of Mount Inasa, five minutes on "the ropeway" (cable car to us), for a 360-degree panorama. There's a restaurant and after dark, as you dine, you can look down at the bay glittering with lights like a multi-stringed necklace, the dark sheen of the water reflecting the brilliant pinpoints.

Nagasaki is perched on the westerly tip of Japan, nearest the Asian mainland, and there are echoes of faraway places in its cuisine: chanpon, a noodle-based mixture of pork and shellfish, claims Chinese ancestry. Portuguese Castella cake is a Nagasaki speciality; Pinkerton, in my book, speaks nostalgically of Castellas and in a shop that claims to have been making them for 400 years, I nibble a delicate square of yellow sponge, and encounter an unexpectedly familiar flavour: Castella tastes exactly like Madeira cake! Why not, since Madeira, too, is Portuguese.

In one of the town's many traditional restaurants – gleaming wooden floors, with low tables and screened alcoves – I enjoyed a simple, perfect sushi lunch beside a tiny internal garden with a trickling pool, a maple tree blazing scarlet. In another I tasted tempura of prawns and vegetables in a batter as delicate as deep-fried lace. I didn't get around to Ohire broth (sometimes made with flying fish) or kamaboko – rissoles made with lizardfish, horse mackerel and sardines.

By chance I discovered Tokiwa, a seafood restaurant with a swimming pool surrounded by diners seated at a counter. But fish, not people, glide in this pool – until a chef in white wellies scoops some out in a net. Minutes later, they're on my plate.

Nagasaki may lack the richness of more obvious tourist destinations, but it has its own appeal. Centuries of foreign influence have shaped a place unlike other Japanese towns: more outgoing, the cultures more mixed. And among the modernity, there are leftovers of history – a jumble of little alleyways lined with old shops; Daikoku, a street-market, three storeys high; a thriving Chinese neighbourhood; memorials to Confucius and crucified Christian martyrs; a fine museum of history and culture housed in a restored Shogunate building.

In the street, stunning girls in pelmet minis clatter by on platform soles as an elderly doorman claps two bits of wood together to signal the arrival of customers in a traditional restaurant. The old and the new co‑exist beguilingly here.

• Butterfly's Shadow by Lee Langley (Chatto & Windus) is out now. It can be ordered from Telegraph Books (0844 871 1515; books.telegraph.co.uk) for £11.99 plus £1.25 p & p £ Finnair (0870 241 4411; www.finnair.co.uk) offers flights from Heathrow and Manchester to Osaka and Tokyo via Helsinki; from £512 return.

• Nagasaki is on Kyushu, Japan's most south-westerly island, with a subtropical climate and spectacular scenery including volcanoes, hot springs and forests.

• Japan experts Audley Travel (01993 838 000; www.audleytravel.com) can arrange tailor-made holidays in all parts of Japan. A two-week tour of Kyushu's highlights, including economy-class international and domestic flights, accommodation and car hire, and taking in Nagasaki, Mt Aso, and Kirishima National Park for hiking and walking, costs from £3,800 per person.

• Independent travellers can buy a Japan Railpass (www.japanrailpass.net) for seven or 14 days and create their own itinerary.

• Nagasaki's Hotel Monterey (www.hotelmonterey.co.jp) is a Portuguese-style hotel close to the waterfront, convenient for sightseeing; doubles from £70 a night, including breakfast. The town is easy to navigate on foot, or by the cheap and convenient streetcar system.

• Dinner at Tokiwa (0081 95 824 2211) costs £20-£30 for a good-value set meal, including some saké. At Yossou (00 81 95 821 1000), a typical traditional lunch restaurant, one course plus drink costs about £15, two courses, £20

• Further information from the Japan National Tourism Organisation (www.seejapan.co.uk)