Andriasang reports that the alternate coloured device will arrive in the territory on March 22, priced at ¥15,000 (£116).
The Cobalt Blue 3DS is the sixth variation of the system to launch in the region, following the Cosmo Black, Aqua Blue, Flair Red, Misty Pink and Ice White.
A Fire Emblem Colbalt Blue bundle has also been announced by Nintendo, featuring a copy of the game and a console bearing its branding. Japanese customers can order the package exclusively through Nintendo's online service for ¥19,800 (£153.25).
Other 3DS bundles coming to Japan this month include red and black beginner packs for Monster Hunter 3G, as well as pink and white Super Mario 3D Land collections.
Nintendo is yet to announce whether the Cobalt Blue 3DS will be available in other territories.
> Nintendo 3DS fastest ever selling console in Japan
Watch a trailer for Super Mario 3D Land below: