Another vendor joined to the Nintendo prepaid card reseller team in Japan the BitCash.
From September 28, 2016 today you can buy different amount of prepaid cards for the Japanese version Nintendo systems (Wii U and 3DS).

On the website you can choose from 500 Yen, 1000 Yen, 2000 Yen, 3000 Yen, 5000 Yen and 9000 Yen worth cards and than you can use them for digital products only in the Japan Nintendo eShop.