The latest report shows net sales have dipped by 8.2 percent year-over-year, falling from 550 billion yen ($4.94 billion) to 504 billion yen ($4.53 billion).
Profits also took a hit, dropping to 16.5 billion yen ($148.4 million) in 2016 from 41.8 billion yen ($376.3 million) in 2015 -- a year-over-year decrease of 60.6 percent.
Looking at software sales for the fiscal year, Nintendo had a number of success stories, including 3DS releases Animal Crossing: Happy Home Designer and Pokémon Super Mystery Dungeon, which sold 3.04 million and 1.22 million units respectively.
On the Wii U, which will be succeeded by the NX in March 2017, the biggest sellers were Splatoon and Super Mario Maker, which each shifted 4.27 million units and 3.52 million units.
Despite some strong performances, Nintendo bemoaned the lack of flagship releases like Pokémon Omega Ruby, Pokémon Alpha Sapphire, and Super Smash Bros., admitting it missed the "energy" they brought to the table the previous year.
In the hardware department, global sales of the Wii U during the fiscal year were 3.26 million, driving Wii U life-to-date hardware sales to 12.8 million. Amiibo sales maintained their momentum on the global market, with figurine-style Amiibos selling 24.7 million units during the fiscal year, and card-style Amiibos selling 28.9 million units.
Going forward, the company is projecting net sales of 500 billion yen ($4.5 billion) and profits of 35 billion yen ($314.7 million) for the end of the next fiscal year, ending March 31, 2017, and is hoping the return of key franchises, such as Pokémon, Kirby, and Metroid Prime, will give it a much needed shot in the arm.
Nintendo is also banking on the continued expansion of its smart device business, and is planning to follow up its first app, Miitomo, with mobile games based on its popular Animal Crossing and Fire Emblem franchises.
"We will release Pokémon Sun and Pokémon Moon globally in winter of 2016. We will also release a number of titles including Kirby: Planet Robobot and Metroid Prime: Federation Force," Nintendo explained in its earnings statement.
"With the release of these titles, we will re-energize the platform and aim to expand our reach globally to a broad audience, including female and younger consumer demographics.
"For our dedicated video game platform business, we're currently developing a gaming platform code-named 'NX' with a brand-new concept, [and] for our smart device business, following Miitomo, we will continuously release new apps in order to expand the revenue base as a business."