Japan has a slightly unfair problem. Tokyo gets most of the attention for its neon-lit streets and astonishingly good restaurants, while Kyoto has more temples and beautiful gardens than any reasonable holiday itinerary can accommodate.

Meanwhile, the rest of the country is left competing for whatever time remains.

And there's an awful lot worth seeing. From beautifully preserved merchant towns in the Japanese Alps to a southern city watched over by an active volcano, some of Japan's most rewarding destinations lie beyond its two most famous stops.

A cruise-and-tour holiday offers a particularly appealing way to discover them, combining longer stays inland with a voyage along the coast. Here are four places worth making room for.

Kanazawa: samurai houses, gold leaf and one of Japan's finest gardens

Kanazawa has an impressive talent for making modern life feel rather far away.

On Japan's western coast, this historic city is known for its beautifully preserved neighbourhoods, traditional crafts and the legacy of the powerful Maeda clan, who ruled the region for centuries.

The Higashi Chaya district is particularly atmospheric, with elegant wooden teahouses lining narrow streets. Nearby, the Nagamachi district preserves the former homes and lanes of the city's samurai families.

Kanazawa also produces much of Japan's decorative gold leaf. Visitors can watch artisans at work or try applying the delicate material themselves, although there's something faintly alarming about being handed genuine gold and told to get creative.

The city's masterpiece is Kenrokuen, one of Japan's three celebrated great gardens. Created over generations, it combines ponds, bridges, carefully sculpted trees and picturesque teahouses. Its name refers to six qualities considered essential to the perfect garden, including spaciousness, seclusion and antiquity.

Even the gardens here have rather exacting standards.

Allow at least a full day, preferably with an overnight stay, to explore beyond the main sights. Omicho Market, with its bustling seafood stalls and local produce, is well worth a visit too.

Takayama: a beautifully preserved town in the Japanese Alps

If Kanazawa feels pleasantly removed from modern Japan, Takayama takes things considerably further.

Surrounded by the mountains of Gifu Prefecture, this small city has retained much of its historic character, particularly in Sanmachi, where dark wooden merchant houses line narrow streets.

Many now contain shops, cafés and sake breweries, making the old town a wonderful place to explore without much of a plan.

In the morning, stalls appear beside the Miyagawa River, selling fresh produce, local crafts and traditional souvenirs. The market has operated in various forms for more than two centuries.

There's also Takayama Jinya, a former government office dating from the Edo period, and the Festival Floats Exhibition Hall, where visitors can admire some of the extraordinarily elaborate floats associated with the city's famous festivals.

They're lavishly decorated with intricate woodcarvings and metalwork, suggesting the local craftsmen weren't particularly interested in doing anything by halves.

Unlike the coastal destinations further south, Takayama requires an overland journey. An organised tour makes it easier to combine with other destinations in the Japanese Alps, and an overnight stay means you can enjoy the old town before the day's visitors arrive.

Nagasaki: the Japanese city with a remarkable international history

Nagasaki's setting is spectacular, with steep green hills surrounding a harbour that has connected Japan with the wider world for centuries.

Long before the modern cruise industry arrived, the city was one of Japan's most important trading ports. During the country's period of restricted contact with foreigners, Dutch merchants were confined to Dejima, a small artificial island where European trade continued under close supervision.

Today, reconstructed buildings and warehouses reveal how the trading post once operated. Elsewhere, Glover Garden preserves the nineteenth-century homes of foreign merchants, offering wonderful views across the harbour.

Of course, Nagasaki is also inseparable from the atomic bombing of 9 August 1945.

The Atomic Bomb Museum and nearby Peace Park offer a moving account of the devastation and its aftermath. They're among Japan's most important historical sites and deserve proper time and attention.

For cruise passengers, Nagasaki is particularly accessible because many of its principal attractions are connected by the city's tram network.

With a single day in port, though, it's sensible to choose between exploring the historic trading districts and spending more time at the memorial sites. Trying to see everything would do neither justice.

Kagoshima: the Japanese cruise port with an active volcano

Most cities have a landmark on the horizon. Kagoshima has an active volcano.

Sakurajima rises dramatically across the bay from this southern Japanese city, occasionally producing impressive plumes of ash that remind residents they're living somewhere geologically rather ambitious.

The volcano is one of Japan's most active, and its influence can be felt throughout the surrounding landscape.

For visitors, one of the best places to appreciate it is Sengan-en, a beautiful seventeenth-century garden created by the powerful Shimazu family.

Its landscaped grounds use Sakurajima and Kagoshima Bay as part of the scenery, a technique known as borrowed landscape. It's a rather effective approach to garden design when you happen to have an entire volcano available.

The gardens also contain historic buildings and offer insight into the region's powerful feudal rulers.

Alternatively, ferries cross from central Kagoshima to Sakurajima in approximately 15 minutes, where visitors can explore volcanic landscapes, observation points and even a footbath heated by the surrounding geothermal activity.

Bear in mind that reaching the ferry terminal from your cruise berth takes additional time, and volcanic conditions can affect sightseeing. For a shorter port call, Sengan-en is a particularly rewarding option.

How to visit these four Japanese destinations on a cruise-and-tour

The appeal of combining a cruise with an escorted tour becomes particularly clear in Japan, where many of the country's most interesting places are nowhere near the coast.

Wendy Wu Tours' 22-day Wonders of Japan by Land & Sea itinerary provides a useful example.

The journey includes overnight stays in Kanazawa and Takayama, with visits to historic districts, gardens and traditional markets. It then continues to Tokyo, where passengers join Sapphire Princess for an 11-night cruise calling at several Japanese ports, including Nagasaki and Kagoshima. Departures are advertised for 9 May and 7 June 2027.

Another option is Wendy Wu's 23-day Japan by Land & Sea itinerary, which combines escorted touring with a voyage aboard Azamara Pursuit, including a cruise call at Kanazawa.

It's worth checking the balance between included guided visits and optional shore excursions. On the Princess itinerary, excursions booked during the cruise are generally an additional expense. Japan is a country that rewards spending time in its smaller cities, particularly where traditional crafts, regional food and local history remain such an important part of everyday life.

Tokyo and Kyoto are wonderful places to begin. But between Kanazawa's gardens, Takayama's old streets, Nagasaki's complex history and Kagoshima's rather restless volcano, there's a compelling argument for making your Japanese holiday considerably longer.