The 3DS sequel was released simultaneously through retail and Nintendo's eShop, but downloads account for just 5% of its launch sales in Japan.
However, Nintendo president Satoru Iwata said that he is satisfied with the figures, claiming that the same-day digital business model has been well received.
He told The Wall Street Journal: "This initial offering going forward, we've gotten a good reaction going."
New Super Mario Bros 2, the first 3DS game to be released simultaneously in digital and physical media, launched in the UK earlier this week. The downloadable edition is priced at £39.99, making it £10 more expensive than a boxed copy.
New Super Mario Bros 2 debuts in North America tomorrow, August 19.
> Read Digital Spy's review of 'New Super Mario Bros 2'
Watch a trailer for New Super Mario Bros 2 below: