The company said its net loss came in at 23.2 billion yen ($229 million) reversing a net profit of 7.1 billion yen a year ago on sales of 571.7 billion yen, which were down 10.0 percent on the year.
Nintendo had previously warned it was on track for an annual loss, reversing an earlier 55 billion yen net profit forecast, as sales for the Wii U came in way below expectations over the crucial holiday sales period.
It said it moved 2.72 million Wii U consoles globally over the 12 months through March, less than a third of its earlier prediction for 9.0 million and dealing a blow to hopes it would match the blockbuster success of the original Wii.
Sales were "not as high as expected", the firm said, adding that price cuts and slower sales of the console's high-margin software weighed on results.
The maker of the Donkey Kong and Pokemon franchises has fallen on hard times in recent years, piling up losses as rivals Sony and Microsoft outpaced it in console sales, while all three companies fight off a trend toward cheap or sometimes free downloadable games for smartphones and other mobile devices.
Nintendo has previously blamed weak earnings partly on high development and marketing costs for the Wii U, which was launched in late 2012, although sales of its 3DS handheld console and related game titles fared better. It cut prices on both consoles to boost sales.
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