Consider the significance of weather in the history of contemporary Japanese art. On the morning of August 9, 1945, cloud obscured the town of Kokura. The crew of an approaching American B-29 Superfortress had planned to drop their payload, given the cartoon-ish nickname of Fat Man, on Kokura, but had emphatic instructions that the target must be visible to the naked eye. Unable to see clearly, they kept going and shortly afterwards completed their mission over a second town, named Nagasaki.

One of those fortunate children of Kokura went on, in 1962, to have a baby boy. She and her taxi-driver husband called their child Takashi Murakami.

"When I was a child, my mother would always talk about that moment, mostly in summer," he says, on a cloudy morning in Hong Kong. "She would say, 'Oh my God, that cloud looks like the one over Kokura.' This is timing! Timing!"

In Japan, they still use the term "Kokura's luck" to mean unwittingly escaping a terrible disaster, but it must surely leave a peculiar imprint if your childhood is spent being told your existence depended on the vagaries of climate. Murakami grew up to become Japan's most successful commercial artist, and perhaps its most laid-back citizen (of which more later). Even if you think you don't know his work; even if you get him muddled up with the other Murakami - that would be the writer, Haruki - you will probably have seen the multicoloured monograms or cherry-blossom designs he began creating for Louis Vuitton in 2003 and which have cheerfully enlivened the wardrobes of fans, and the coffers of knock-off merchants, ever since. Failing that, you may have glimpsed the Google doodles he did to mark last year's summer and winter solstices. Once you start looking around, his creepily cute mushrooms, flowers and critters are everywhere.

His fame rests on his ability to make Japanese mass culture desirable, even artistically important. He's usually cited as one of the trinity of artists, along with Jeff Koons and Damien Hirst, who've done more to bring their particular version of art to mass attention than any others. Andy Warhol is the frequent comparison but Warhol lived in a prelapsarian world of landline telephones and faxes. The imaginings of his artistic heirs can girdle the globe in a second. Perhaps that's their good fortune. It's certainly good timing.

Murakami is in Hong Kong to promote his latest exhibition, at the Gagosian Gallery in Central, entitled "Flowers & Skulls". As is the way with major galleries nowadays, there are few helpful labels sullying the walls: you have to figure out which work is which by using a numbered floor-plan. Five of the nine recent ones are listed as "Yet to be titled, 2012" and it says a good deal about contemporary art that you might well believe those are the titles. (The gallery confirms the works are awaiting official names.) No reference is made to how much they cost and several of the earlier works on show aren't for sale, they're on loan.

Murakami, sitting in a back room with an interpreter, looks stoic, as if about to endure some tedious but necessary medical treatment. He's wearing a cap ("made by a friend"), a pair of vintage Italian army trousers, no socks and a jumper that he pulls over his tummy, several times, to show how much weight he's put on. When asked a question, he closes his eyes tightly and his knees begin shaking; in this respect, he resembles the little boy in the classroom who jiggles when he's furiously concentrating, the one who's slightly obsessive about the things he does, the one who doesn't quite fit in.

"I'm totally the same as Japanese geek," he announces at one point, in somewhat broken English (early in the interview he decides to strike out alone on the translation front). "But my main job is contemporary artist. That's why I go to the shower every day - I have to be with the people!"

As it happens, "Little Boy" was the title of a Murakami show at the Japan Society in New York in 2005. It referred to Fat Man's sibling, the atomic bomb dropped on Hiroshima three days before Kokura had its narrow escape. The show's subtitle was "The Arts of Japan's Exploding Subculture", and it was the last instalment of Murakami's "Superflat" trilogy, Superflat being the movement he initiated in 2000 after choosing it as the name for a group show he curated at the Los Angeles Museum of Contemporary Art.

The reference was, initially, literal: Murakami felt that Japan's defeated, post-war, animation-driven culture was 2D, unlike the 3D, victorious empires of the West.

"I like to emphasise one important thing," he says, urgently. "The reason Americans and British can create contemporary art is because they won the war. This is superflat. After the bubble-economy in Japan, in 1987, we have a chance, but before then - no chance."

Superflat has, with no apparent irony, sprouted all sorts of knobbly semantic tentacles. It seems it can now refer to a horizontal flattening between genres; a vertical flattening between high and low culture; a melding between cute and pornographic; shiny planes of colour; Japan's culture of superficiality; and even to the popping of an economic bubble.

To the outside world, however, superflat is more likely to be regarded as a byword for what happened at Fukushima, on March 11, last year, the closest Japan has come to a non-cartoon, real-life nuclear disaster in Murakami's lifetime. How does art theory move on from that?

Murakami closes his eyes for a long moment.

"The answer is super-difficult," he says, politely, after a while.

Where was he on that afternoon?

"I was in my studio in Saitama [about 25 kilometres north of Tokyo]. People were holding the paintings during the earthquake, everyone understood immediately. One of my assistants, very nice, says, 'You have to hold it as it's drying.'"

So the work came first? "Yes!"

Murakami laughs. He has three studios and about 90 employees, all of whom do a calisthenics routine when they clock in for work each morning.

"I said to my assistants, 'Please go to 7-Eleven or convenience store to get stuff, toilet paper', and they buy some. There were 35 assistants, then they ask if they can go back home. But at night-time, they start to come back because trains not moving. Twenty come back. We survive three or four days like this."

In April, when Time magazine asked him, as one of its "most influential people", to name the most influential place in history, he chose Fukushima. Of Japan's reluctance to halt nuclear energy, he wrote, "I feel that this dilemma is much like that of a country that wants to end a war but cannot."

Perhaps he, too, feels trapped by old pre-occupations. In February, at an exhibition in Qatar entitled "Murakami - Ego", he showed a three-metre-high, 100-metre-long work entitled Arhat, the Buddhist term for someone who has reached nirvana. It was a massive visual reference to Fukushima's sufferings, and it was meant to be viewed like a scroll, which, after all, can be both flat and three-dimensional. Despite the fact that 200 people had been working on it, it was also unfinished. (Mr DOB, the cartoon-icon he created in the 1990s, could be seen spectacularly vomiting in another room as if, literally, sick of himself.)

Was Arhat intended to be his Guernica, Picasso's 1937 painting of the eponymous bombed village, which brought attention to the atrocities of the Spanish civil war?

"Good example," says Murakami, after another shut-eyed pause. "Twenty years ago, I was an anti-nuclear activist, then I become an artist. After Fukushima, I super-remember I gave up anti-nuclear movement but now - I can make the painting! When someone sees Guernica, they learn about history. In 100 years, someone sees my painting, they learn the history. It's super-unusual, it's far away from my series of paintings. It was about witnessing the new religion emerging and the natural environment - you need something to comfort the people."

"Flowers & Skulls", however, is not a continuation of this enlightened, post-Fukushima spirit.

"Honestly, I don't think so," says Murakami. "This is a conceptual show, that's why the title has almost no meaning. Flowers and skulls? What does this mean?"

Well, if he doesn't know … "Means I want to present this show as a structure, an art structure, my gift for the Hong Kong people," he says. "Before, I try hard to present to the Japanese audience but I give up now. Japanese people always looking for storyline, not structure."

(Seeing as he's drawing distinctions: are the islands Senkaku or Diaoyu? The interpreter draws in her breath, then gives a little laugh. After a moment, Murakami replies, mildly, "I'm Japanese person. I have to say it's Japan. But I have no information from each country.")

There are two self-portraits in the show, each consisting of several cartoon images of the artist. Murakami - goateed, pony-tailed and bespectacled - looks mildly intoxicated, or possibly exhausted; and the Japanese speech bubbles ("Right now, we are really in a bad mood. We are seething with anger at the irresponsible behaviour of our studio staff"… "I long wanted to paint my own pathetic self"… "If we take Andy Warhol as an example, in the Western art world, he is appreciated mostly for his Duchampian cynicism and deconstructive architecture but in Asia it seems as if he is popular simply as a famous brand") read, in English anyway, like the verbose ramblings of the last man in the bar.

Murakami, however, doesn't have a home. He nests, geek-style, in his studio. "When you come to my studio, you see my bed-box," he remarks. "You know Tempur? Very, very expensive?" Tempur-Pedic, the mattress company? "Yes! I sleep on that mattress." But where's the privacy? "Closing the eyes. That's why I enjoy the escape into fantasy."

He also has a classic geek-hobby: cultivating cacti; although he admits that, as cacti aren't overly keen on the Japanese climate, of the 300 he had a decade ago, only 30 survive. Apart from that, his single non-work-related occupation would appear to be visiting the doctor. "Each week, I go to the hospital for the check-up," he says. "Doctor say I have good health but I say, 'I have pain here, I can't see, I have noise in the ear, I have headache.' Doctor say, 'Don't worry.' But I have a mania."

You have to wonder whether, in all of this, there's any joy.

"Good question," he says. "It's painful. I'm not enjoying. I'm an astronaut. What is feeling in space? Great! But training-time is super-painful and every day I'm training. Like astronaut, watching through the window, you have one moment when you think, 'This is the real thing.' When I finish something, I understand this feeling for one second, two seconds."

Art critic Midori Matsui has said of Murakami, "I think he is a very lonely person and he needs to create his own family." This insight, when read back to him, elicits a derisive snort from the artist.

Still, it's true that he likes to surround himself with young, talented artists, who then go on to have their own careers (his assistants' names are written on the back of his works) and since 2002 he's organised an art fair called Geisai in both Tokyo and Taipei.

"Why don't I have money? Because I spent US$20 million on Geisai! Yes! Just for Geisai! Crazy amount of money - this is like car-racing!"

That makes him sound like a disorganised spendthrift, which he isn't. He's shrewd in his business dealings: he controls the release of images from his studios and was the first Japanese artist to negotiate royalties on resales of his work at auction. His career - branding himself as an Eastern artist in the West, then re-introducing himself, the benedictions of the West upon him, to Japan and the rest of Asia - has been carefully plotted.

In April, there'll be a departure: he's launching a film for children called Jellyfish Eyes. He's done animation before (perhaps, most famously, a music video for Kanye West, who's said to be a fan of Hiropon, the Murakami sculpture of a lactating woman so unfeasibly large-breasted and narrow-waisted she could only be the midnight product of a fevered geek imagination). This, however, is his first live-action, 90-minute work.

"Stupid, stupid movie!" he cries, grinning. "Maybe my auction prices will drop down. But at the moment I'm super-happy, super-excited, super-eating-a-lot!"

Did he have to visit the doctor while he was making the film? "No!"

The premise - he says it's about young children who each carry a monster around with them in a "device" - sounds like a psychoanalyst's dream. There's no mention, yet, of what the weather's like as the youngsters go about their business but it seems Fukushima will be relevant. It's set in the future. You can be sure it will reference the past.


Takashi Murakami's "Flowers & Skulls" exhibition will be on display at the Gagosian Gallery (7/F, Pedder Building, 12 Pedder Street, Central, tel: 2151 0555) until February 9.