The Wii U sold just 160,000 units worldwide during the three months ending June 30th.
During that same period, the firm reported software sales of just over one million.
Wii sales for the last quarter meanwhile were at 210,000, with software sales hitting 3.67m.
Nintendo pinpointed lack of Wii U sales on the dearth of first-party titles, which it felt otherwise would have “strongly” driven hardware sales.
It said that overall, Wii U hardware sales were still having a negative impact on its profits.
Despite a lacklustre quarter for its home console, Nintendo still expects to sell nine million units by the end of the year.
The 3DS continued to enjoy success, selling 1.4 million units in the three months ending June 30th, and shifting 11 million games.
Leading titles for the platform include Animal Crossing: New Leaf with sold 1.54m units worldwide in the last quarter, with 1.19m of those outside of Japan.
Thanks to the performance of the 3DS, net income for the last quarter reached £58m, up from a loss of £116m during the same period last year.
Moving forward, Nintendo said it would attempt to concentrate on proactively releasing first-party titles from the second half of 2013 through next year, starting with Pikmin 3, which has been received positively by critics.
Other titles in the pipeline include The Legend of Zelda: The Wind Waker HD, Donkey Kong Country: Tropical Freeze, Super Mario 3D World, Wii Fit U and Wii Party U.
It also said it would look to improve the profitability of the hardware by reducing its costs.