Most of Yakushima was logged at some point, starting early in Japan’s Edo period (1603-1867), but the forest has been conscientiously replanted since logging ended in the late 1960s.

Having sailed in and tied up our boat in the fishing port of Anbo, one of two small towns where most of the island’s 13,486 inhabitants live, we enter the forest at the Yodagawa Mountain Trail Entrance, clutching maps found at the tourist information office.

The staff promised that if we walked in a clockwise direction at a moderate pace for three days, the path would lead us past mountain huts where we could find free shelter, across the island’s highest peak and eventually to a bus station, where we could catch a ride back to a hot shower and a cold beer in Anbo.

Our first day of hiking is just an hour’s walk to the Yodagawa Hut, where we unroll our mats and sleeping bags.

Yakushima’s mountain huts, which can each accommodate up to 40 hikers, are very basic; they have sleeping spaces marked out on a wooden floor and a few grimy windows letting in the dim forest light. There is no electricity, nor any cooking facilities, and only one reeking drop toilet per hut.

Having settled in, we follow the sound of water down to a narrow river that winds around the hut. It is crystal clear and numbingly cold, with the forest tumbling down to the very edge.

Heavy, gnarled tree branches reach across the water, and those that have fallen are rotting underfoot, covered in thick fluffy moss.

The forest hums with the sound of birds and Yakushima’s indigenous subspecies of the Japanese macaque. All fall silent, though, as the sun sets and the forest quickly turns dark.

We return to the hut and cook a simple meal on our camp stove. With campfires forbidden by park rules, and stilted conversation with the one other hiker who can speak a little English having run its course, we are soon in our sleeping bags.

It is frigid the next morning, but at least it is not raining. Yakushima gets more than twice as much rain per year as the Japanese mainland, making us thankful for every hour of sunshine.

We fire up our stove for a quick bowl of porridge and then hit the trail.

For the first few kilometres it winds through heavy forest. Cedars are interspersed with smooth-barked tall Stewartia, tsuga conifers and Japanese wheel trees, which wrap themselves sinuously around the trunks of other trees.

The trail is rugged, with sections requiring the use of hands and the frequent fixed ropes. Roots and rocks underfoot slow us down to an average pace of 1.5km/h (1 mile per hour) – as predicted on our maps.

We refill our water bottles in the clear, cold streams, remembering how staff at the Anbo camping shop at which we rented our backpacks boasted of Yakushima’s “soft sweet mountain water”.

By midmorning we are hiking in scrub-covered highlands dotted with bright pink and white Satsuki azaleas, a type of rhododendron; entire valleys are carpeted with the flowers. Walls of mist roll in to hide them for a few minutes, then bursts of sunshine burn off the mist and reveal the colours once again.

By noon we have scrambled up 1,936-metre (6,350ft) Mount Miyanoura, the tallest peak in the Kyushu region. Ninety per cent of Yakushima is mountain slope, with many of its peaks topping 1,800 metres, earning the island the nickname “The Alps on the Ocean”.

The granite has been eroded into odd, often humanlike shapes that thrust out of the green, flower-dotted landscape.

From Miyanoura we turn east, dropping into a valley towards the Shin-takatsuka Hut, which stands at an elevation of 1,480 metres.

We once again claim spots on the floor and cook dinner on our camp stove, interrupted only by a docile yakushika, a subspecies of sika deer, that wanders through the camp, munching moss.

Hiking – or haikingu, as it is known in Japanese – is particularly popular with Japan’s elderly, who hike in groups and bring a spirited sense of community to the huts.

They all rise from their sleeping bags with loud greetings and commotion at 4.30am, and arrive at the next hut by midday, earning themselves an afternoon of lounging in the often crowded, uncomfortable facilities.

We start later, take longer breaks on the trail and arrive at each hut in the late afternoon.

On our third and final day of hiking, we enter the ancient Yakusugi cedar forests that Yakushima is famed for. Here there are better maintained trails crowded with walkers, as many of the island’s oldest and most famous trees are accessible on day hikes.

The forestry department has designated and mapped 37 particularly impressive yakusugi (cedars that are more than 1,000 years old) and kosugi (“child cedars”) that are sought out by hikers.

The first we encounter is Japan’s oldest tree, the jomonsugi, which scientists estimate to be up to 7,200 years old.

It is named after the Jomon period which ended around 300BC, and historians believe it may have escaped logging because of the irregular shape of its massive trunk, which is five metres in diameter.

The trail then takes us past Wilson’s Stump, all that is left of a massive cedar felled for timber in 1586. Named after British botanist Ernest Henry Wilson, who told the world about the hollow stump in 1914, it is 4.4 metres across at chest level and contains a small shrine.

By midmorning we have seen many of the island’s famous trees but are having to stand aside as day-hiking tour groups huff and puff their way past us and up into the mountains.

Gnarled, moss-covered cedars and a clear stream tumble down through the ravine, but as each step we take becomes easier, with better signage and even handrails, we feel the magic of the more remote mountains fade.

Having seen Yakushima’s interior, we want to explore the coastline, so rent a scooter to travel the road that rings the island.

We stop at a natural onsen that is accessible only at low tide – at other times the sea floods the mineral pools – and a lighthouse built in 1897.

On the west side of the island, the narrow, winding route becomes a “World Heritage Listed Coastal Road with Wildlife”, where we have to slow down because of the number of deer and monkeys lounging on the tarmac: a different kind of magic.

Most visitors to Yakushima arrive by ferry from Kagoshima at either Anbo or Miyanoura, or via the island’s small airport, which is served by flights from Itami, Fukuoka and Kagoshima.