The Big N has removed a small-time game from the Nintendo eShop after it inadvertently led to a hacker enabling the use of homebrew games and apps on the 3DS.

Joystiq reports that Nintendo has axed Cubic Ninja from the Nintendo eShop of Japan recently. This 2011 3DS game was only released digitally for the Japanese market, otherwise it was available for relatively cheap as an oftenly overlooked title. A hacker was recently able to use a modified save file and digital copy of Cubic Ninja in order to unlock the use of homebrew games and apps on the Nintendo 3DS handheld.

Nintendo has since removed the game from its digital market, but can't really do much about its physical copies that have been collecting dust on store shelves for the past three years. Of course, third-party retailers have now started up-selling the offbeat game to take advantage of everyone hoping to hack their handheld. The Big N is scared that this will lead to a surge of piracy of its commercial games on the 3DS via emulation software, which was a huge problem for the regular DS handheld.