When Hayao Miyazaki announced his retirement from Japan’s greatest animation studio in 2013, his young protege Hiromasa Yonebayashi wasn’t worried. The master had already retired five times before. “He was always saying, ‘Oh this could be the last film.’” Yonebayashi shrugs. “He’s still in the office.”

You get the feeling that’s not entirely a comfort. Miyazaki is not the only director at Studio Ghibli, the animation company he co-founded in 1985, but he is behind the three most successful Japanese anime of all time. Princess Mononoke was Japan’s highest grossing film until Titanic – bested four years later by Spirited Away, the first non-western film to win the animation Oscar. Miyazaki’s career has been built on drawing the mutual awe between humankind and nature: no wonder he inspires David Attenborough levels of devotion in Japan.

Ostensibly, his mantle has now been passed to the man perched on a London hotel sofa before me, a slightly awkward 42-year-old in a flat cap with two directorial credits to his name. Even the studio seem faintly concerned that Yonebayashi, despite having landed an Oscar nomination for When Marnie Was There, doesn’t stand quite as tall as Miyazaki: he is accompanied by producer Yoshiaki Nishimura, to flex a bit of corporate Ghibli muscle.

In true studio tradition, When Marnie Was There boasts a young female protagonist, Anna, who isn’t trying to win over a boy and isn’t even particularly nice. A reclusive girl with an undiscovered talent for drawing, she is sent by her harried single mother to live with her aunt and uncle in the countryside. There, she discovers an abandoned manor house that springs to life to reveal the beautiful, princess-like Marnie, Anna’s spirit guide to a more glamorous existence.

Neither Marnie nor Anna are saints (though Marnie may be a ghost), but part of the film’s appeal is how it generates sympathy for the unsympathetic. “That was actually the most difficult part,” says Yonebayashi. “But you can see Anna grows up a little bit – at the beginning she can’t see eye to eye with anybody, but by the end she can see and talk to another person.”

Like 2010’s Arrietty, which took inspiration from The Borrowers, When Marnie Was There is adapted from a British children’s book, its characters transplanted from Norfolk to Sapporo but Marnie, crucially, is kept as a westerner. “One is Japanese and one is a blonde foreign girl,” he says, “but in the end I thought that added another dimension.”

Made in the wake of the 2011 Japanese earthquake and tsunami, the film is full of references to a conservative ideal of Japan: a traditional festival, an idyllic countryside, and a secret that connects Anna to her ancestors, through which she learns to accept herself. “So many people lost their lives and so many others lost loved ones,” Yonebayashi says. “Anna loses her relatives as well.”

Female-led … Spirited Away. Photograph: BFI

So is Anna Japan? Yonebayashi cocks his head and gives the longest and quietest of many pauses. “Could be. Anna is a lonely girl. At the moment, so many Japanese people feel lonely even though they’re connected by technology. I’m not sure if Anna and Japan itself are the same, but people in Japan should be able to understand her.”

He describes Anna as “an androgynous character, in the transition between child to adulthood, a very sensitive age” but offers up an intriguing reason for choosing another female-led story : “I’m male myself, and if I had a central character who was male, I’d probably put too much emotion into it, and that would lead to difficulty in telling the story.”

Will Ghibli ever employ a female director? Nishimura fields this question. “It depends on what kind of a film it would be. Unlike live action, with animation we have to simplify the real world. Women tend to be more realistic and manage day-to-day lives very well. Men on the other hand tend to be more idealistic – and fantasy films need that idealistic approach. I don’t think it’s a coincidence men are picked.”

It may be a moot question if Studio Ghibli’s financial struggles continue. The company was groundbreaking in the 1980s for hiring full-time staff rather than drafting in contractors: an expensive production model that allowed Ghibli to train the next generation of brilliant animators, including Yonebayashi himself.

Now Ghibli is facing the hard industry truth: hand-drawn animation is ever more expensive and risky to make, especially not outsourced to cheaper countries. Even Miyazaki has tacitly admitted as much – a short film made for the Ghibli museum in Tokyo will be his first in full CGI. The studio’s next feature is a collaboration with Europe’s Wild Bunch studio directed by Dutch film-maker Michaël Dudok de Wit.

“The slim-down process has begun,” says Nishimura. “There is no in-house production at the moment. As for the shadow of Miyazaki, we must feel his presence, as well as that of Takahata-san, the two maestros who established Ghibli and gave not just Japan but the whole world courage. It’s not just the technique of animation – it’s the storytelling, what we tell, who we tell, and the aspiration of that film-making. That’s what we have to carry on.”

For now, Miyazaki’s Oscar stands alone on the shelf: Yonebayashi lost at last year’s awards to Disney Pixar. But tellingly, Inside Out was an honest story about a young girl. Miyazaki has already trained the next generation, in more ways than one.