UPDATE #2: Nintendo has responded to Eurogamer regarding its Japanese arm's decision to not allow indies to self-publish and blamed the decision on the company's Japanese licensing department.
But Nintendo did not explain why the department had made this decision.
"The policy in question is the decision of Nintendo's department responsible for licensing activities in each region," a company spokesperson confirmed. "The licensing department of Nintendo Co., Ltd is currently not accepting subject applications from individuals in Japan."
UPDATE: I reached out to Japanese indie game expo BitSummit's director James Mielke to hear his thoughts on the matter. His reply is as follows:
"I wouldn't read too much into it. It's not to say Nintendo won't eventually open things up. When you've got franchises like Mario and Zelda, you have to maintain a certain quality control. But you'll note in that leaked document that it says 'developers located in Japan at this time.' Nintendo may simply still be tailoring their approach or legalese to Japanese indie developers. But I do hope they have something in store, because indie development is the water that fills a game library's riverbank. You can be a giant rock sitting right in the center of it all, but that water will flow right around you down other channels if you don't open yourself up to it."
Original Story: Nintendo has recently opened its door to indies and allowed for self-publishing, yet for whatever reason the hardware manufacturer isn't currently accepting submissions from Japanese indie developers.
This recent tidbit was discovered in the fine print of a GDC survey for potential Wii U developers where it noted, "We are not accepting applications from developers located in Japan at this time." (Thanks, Kotaku!)
This may seem bats*** insane given that elsewhere Nintendo is not only allowing self-publishing, but waiving the usual licensing fees associated with publishing a game developed on Unity. Furthermore, Japan has been the home of some of the best indie games over the last several years with such daring hits as Cave Story, La-Mulana, and Tokyo Jungle.
Kotaku noted that a month after applying to become a registered Wii U dev Studio Rice Cake was sent an e-mail from Nintendo in the spring stating that it was difficult to support indies in Japan. "Seeing 'No Japs' written on an international-looking website is such a terrible sight that it makes me weep," tweeted a developer from the studio.
I've reached out to Nintendo to explain its policy with Japanese indies and I'll update as I hear back.
For more info on the Japanese indie scene, EG-contributor Daniel Robson took a look at the Kyoto-based BitSummit indie festival this spring.