The link arrived in an email; my sister Jenny saw it first. “Tokyo – learn the way of the ninja.” I opened it, closed it, opened it again while my stomach did a few flips. For someone weaned on martial arts movies, who imagined his father’s raspberry patch into a gang of bloodthirsty assassins (didn’t go down too well when I hacked them apart with a homemade bamboo sword), this felt like what my life had been building up to.

What I didn’t realise was that in less than a month I would be learning to throw stars, wield a sword and wrestle in a sumo loincloth, on a bespoke journey that would stretch my tendons as well as my horizons.

There’s much more to the art of the ninja than our idea of black-clad assassins. Historically, they were deployed more as undercover spies, and the one style of fighting that has represented their martial arts expertise in the west doesn’t even begin to tell the story of what is an entire way of life rather than just a sparring technique. Some of it is incredibly subtle; all of it is deeply enmeshed in the history and Zen philosophy of bushido, the Japanese way of the warrior.

The first stop on this adventure, then, would be Kyoto, medieval capital of Japan and locus of much traditional culture. My first full day was largely spent in discussion of the concept of wabi-sabi with my guide, a former Zen Buddhist monk, as we wandered the city’s profusion of temples and gardens. The first part of the word, wabi, is tough to translate, but absolutely integral to appreciating Japanese aesthetics: nowadays it means sort of fresh, or rustic, while sabi is the beauty that comes with age, such as the patina on a rusting gate. Wabi-sabi is at heart the idea of finding something beautiful precisely because it is flawed (and so becomes a meditation on the impermanence of life, the inevitability of change, and so on).

This was followed by Zen meditation with a US-educated priest and instructor, Reverend Takafumi Kawakami. The experience of Zen – an empty mind, and total clarity – can come from any number of things: walking, running, martial arts, art. These are all potential catalysts that allow the mind (if you’re lucky) an escape, even a momentary one, from chatter and clutter.

Kawakami is a proponent of zazen, seated meditation. It’s not easy – you don’t sit so much as kneel, bum on heels, which is tough after a while – and Kawakami has a “compassion stick” that is used to wallop anyone in need of a little focus (or whose knees are starting to give up the ghost). Actually, it is a beautiful 15 minutes of concentrated, dedicated un-thought. As we kneel in a small studio, he slides a shoji screen open to reveal a little garden, lights an incense stick to help us keep track of time, rings a small bell and we begin to meditate. At first it almost feels comic to just sit and try not to think. But then the patter of the rain and the croak of frogs in the pond recede, and the world’s clamour fades.

Afterwards, Kawakami walks us round the temple. The spaces are punctuated with incredible gold screens painted with obscure Christian iconography. Then it is back for a delicious meal of fish and grilled vegetables at Touzan, one of three excellent restaurants at the Hyatt Regency, designed by the iconic contemporary architect Takashi Sugimoto – who also, somewhat incongruously, calls himself Super Potato.

One bullet train ride later, the next morning finds me slightly bleary eyed in a small alley off a quiet Tokyo side street: we’re doing early training at the sumo stable, or dohyo, which is unlike any gym I’ve ever seen. Eight wrestlers stand around the edge of a dirt ring. Watching them from a small platform, accompanied by a remarkably well-fed cat, is their master, arms folded, unimpressed and perfectly still.

Their rounds of conditioning look incredibly tough – while one braces, the other’s job is to push him out of the ring, feet scraping for purchase. Expressions range from unruffled and implacable, even with someone else’s hand on their throat, to a savage mien, twisted with exertion. Realising the skill, power and flexibility they’re using to move not just their weight but their opponent’s, I am somewhat in awe of their strength.

There’s no talking, except when the coach, in a lime-green T-shirt, breaks his stern pose to scratch his sumo-fat cat’s ears and bark out some order or advice. I’m ushered into the shower room by two wrestlers, who wrap me up in a stiff canvas mawashi with a distinct feeling of school-lost-property-basket to it. I go back into the dohyowith the others and, acutely aware of my naked long legs and skinny arms, join in. There’s one exercise where I have to slap and push with my whole core at a tree trunk concreted upright in the corner of the room. There’s lots of stretching and leg-stamping, then traversing the ring in a deep squat, sliding my feet in a sort of duck-walk shuffle, elbows in at the sides, knees aching and thighs shaking. It’s hugely tough – and my companions have already been going for two hours.

Then it’s my turn to actually wrestle – with the big boy. My stomach flips. It’s like a scene from a James Bond film. One of the stable’s biggest wrestlers is standing there, owning the ring, one eyebrow slightly raised – in the international language of alpha posturing, it says, “What’ve you got, Dyson?” He strides slowly to one edge of the ring, braces his legs for impact and slaps his chest, motioning at me to come at him. I bend my knees, summoning my energy for one burst, and go for it. Pushing as hard as I can, I dig in and somehow slide him backwards, one step at a time, but it’s exhausting. And he’s certainly not making it easy. Finally, I do enough to push him out. He smiles, steps back in, taps his chest. Again.

Bright red in the face, eyes popping, forehead smashed into his solar plexus as I shove him across the ring a second, third and fourth time, I’m doing my best yells and roars. By the fifth and sixth times, my knees feel like they’re coming undone, the yells have devolved into the mewling of a new-born kitten and I’m just wanting it all to stop. Then, just as he’s near the boundary of the ring, and I’m considering giving up because I’m pushing as hard as I can but it’s simply not working, I see one enormous shovel-like hand wind up to swat me across the room. There’s absolutely nothing I can do about it.

I go tumbling, falling hard into the dirt, but I’m in one piece (bar a scratched knee), and I’m elated. I suddenly realise: I’m covered in sweat and dirt in a genuine sumo stable in the backstreets of Tokyo. This is beyond even the promised “authentic experiences” from fancy travel operators; I’m quite literally living a childhood dream. I have a couple more cracks and end up on the floor at least once more before the coach brings it to a close. I stand there in my mawashi, notebook in hand, (shaking) pen in the other; I have trouble stringing a sentence together, let alone any questions. Not a day I’m about to forget.

We part company with smiles, laughs and backslaps and I head back to Tokyo’s Park Hyatt. If you’ve seen Lost in Translation, you’ll know the hotel. With its gobsmacking view over the city, it’s the perfect counterpoint to the very traditional martial artists I’m meeting. A much-needed swim and steam, and I’m ready for my first class with a ninja master.

It’s a 40-minute rush-hour train ride to sensei (teacher) Yamamoto Shunji’s apartment in Tokyo’s Setagaya-ward, just round the corner from his Bujinkan dojo, and the meeting is a revelation. Kneeling on cushions and sipping tea, the sensei and I chat about the history of ninja and the other warrior arts, from the martial – sword, spear and knife as well as concealed and improvised weaponry – to the artistic, which include calligraphy, meditation, poetry and music. This is more in line with the ideal skills of the medieval knight that I had thought.

In the old days, he says, ninja were also known as rappa, which is written using the kanji symbols for “disorder” and “waves”. They were expected to be good at “100 things” (something Yamamoto takes seriously – in his spare time he is also a percussionist and a jazz flautist; a gold flute sits next to his sword rack). The whole thing is rather dreamlike – after showing me exactly how one should hold a shuriken(not so much a throwing star as an easily concealed and versatile knuckle-duster), he plays a few riffs on his flute and we wander off to the dojo.

It’s quite a small class, just six students, and over the next couple of hours we look at elements of kyusho (pressure points) and atemi(strikes and joint manipulations). Sensei dances around like a spry, mischievous uncle, chuckling as he shows me different moves – distraction blows, disarms and joint locks. One quite bizarre one, administered in the dimple of my chin, is agonising, but only momentarily; another is a crippling grip delivered – along with an apologetic smile – to three points of my forehead, which collapses me in a second. There’s an unsettling moment when I seem to have him wrapped up, but out of nowhere his foot whips up to stop millimetres from my chin; and I find it rather uncanny when he shows me some incredibly simple locks that can be done with just a piece of string.

Crucially, though, it is all incredibly good-natured and open. The collegiate atmosphere as we work through various self-defence applications often dissolves into giggles because, as sensei says over tea, the class should be fun – you learn more if you enjoy it.

That’s not to say that the discipline itself is light-hearted. Five of the basic tenets of ninjutsu taught in his school are jin, gi, shin, dei and chi – loosely translated as compassion, justice, determination, courtesy and wisdom – which are represented in the five pleats of the formal Japanese hakama trousers, and essential to bushido, the way of the warrior.

“What you do when you first go into a dojo is really important,” he says. “First, meditation; then bowing. This shows a clear state of mind and that, if both are bowing, you cannot attack each other. Then you learn how to defend yourself. But in doing that, you also learn how to hurt people. And in knowing what hurts people, you become more compassionate.”

I left feeling energised and enthused, if sporting a couple of new bruises and scratches. But this session, and the one the following day, were conducted with charm and positivity – and, importantly, left exactly the right sort of questions.

Some of these were answered at the Jidai Academy in Kita-ward, the next dojo I attended for an introduction to traditional samurai weaponry and kenjutsu (sword techniques). Waiting in a small, dark room with a squeaky floor and an astonishing array of weapons lining the walls, I was slightly unnerved to be met by not one but three people in full, movie-style ninja dress, complete with black masks (the master asked to remain anonymous).

Again, they emphasised that ninja were not so much stealth assassins as spies, but, having dressed me up in similar masked garb, we worked through applications of throwing blades, disabling techniques using chopsticks, some knife and other blade work, and specifically how to attack someone who has traditional training. The ninja’s special skill, really, is to think outside of the box and do the unexpected. In a land famed for its strict adherence to tradition in all things, you can see how effective a technique that might be.

There’s an unforgettable moment when, having moved from blowpipes and sticks to practising how to evade and then attack someone with a sword, I am told to do a sort of somersault diagonally past the blade, practice dagger in hand, then spring manfully to my feet behind the assailant and stab him in the neck and shoulder. Feeling acutely aware of my six-foot-six frame in relation to both the studio and my opponent, I manage a slightly awkward forward roll (something, it should be noted, I haven’t attempted since primary school gymnastics), accidentally belt the guy in the side of the knee as I lurch to my feet, and swipe at his throat. Slightly dizzy from all the spinning, I turn around to the remarkable sight of the three masked ninja politely clapping.

As the practical demonstrations and participation continue, I feel more and more like I’m in my very own film. We delve deeper into the armoury, trying things out, talking about the history of different styles and weapons, learning by doing, comparing the sensei’s moves with European fighting styles. The ultimate goal in bushido is an ippon, victory in one movement or strike, regardless of the personal cost – something that is hammered in over a session against a padded practice sword. For ninja, however, it was about being able to sidestep that strike, to live to fight again.

The political intrigues that once begat the arts of the ninja might no longer be relevant, but the state of mind is one that will always be vital. Seeing them in action, and also seeing how the tenets of all the artists I met permeate their lives, I began to understand what Zen is and why these practitioners see it as something worth pursuing. Now I just need to remember to default to meditation – not pressure-point strikes – when my boss gets to me.

Jack Dyson travelled as a guest of Black Tomato (0843-636

8049; www.blacktomato.com), which offers seven nights in

Kyoto and Tokyo from £4,599 per person, including private

transfers, guiding and training, international flights with Qatar Airways, and accommodation and breakfast at the Hyatt Regency Kyoto and Park Hyatt Tokyo. All aspects of ninja and samurai

training are tailored to suit interests and ability.

Hyatt Regency Kyoto, 644-2 Sanjusangendo-mawari, Higashiyama-ku, Kyoto 605-0941 (+8175-541 1234; www.kyoto.regency.hyatt.com), from £154. Park Hyatt Tokyo, 3-7-1-2 Nishi Shinjuku, Shinjuku-ku, Tokyo 163-1055 (+8135-322 1234; www.tokyo.park.hyatt.com), from £315.

British Airways (0844-493 0787; www.ba.com) flies from London Heathrow to Tokyo daily, from £555 return. Qatar Airways (0844-846 8380;www.qatarairways.com) flies from London Heathrow to Tokyo via Doha up to four times daily, from £529 return.