Nintendo of Japan is currently not accepting submissions from the country's inde developers due to the policies of its licensing department.
In a statement to Eurogamer Nintendo commented, "The policy in question is the decision of Nintendo's department responsible for licensing activities in each region. The licensing department of Nintendo Co., Ltd is currently not accepting subject applications from individuals in Japan."
Quite why Nintendo's Japanese licensing department made this decision is however unclear. Nintendo in other regions is not only allowing indie developers to make applications but it's also waiving the usual fees associated with releasing a game on Unity. The company has also dropped the requirement that developers must have a dedicated stuio – allowing indies to develop from home.
Japan has also seen some excellent indie games over the last few years including Tokyo Jungle, Cave Story and La-Mulana.
Studio Rice Cake, a Japanese indie, was sent an email a month after applying with Nintendo informing the developer it was difficult to support indies in Japan.
The company's decision not to support indies based in the region was revealed by a post-GDC survey.