Wii U sales during Nintendo's first financial quarter totalled just 160,000 units worldwide.
The latest Wii U hardware sales figure represents a significant decline from Nintendo's previous financial quarter, when the company also fell short of its target with 450,000 Wii U sales.
Lifetime Wii U sales now stand at 3,610,000, some way short of the 5.5 million sales Nintendo initially expected by the end of April.
Nintendo said Wii U's underperformance was "mainly due to the release of few key first-party titles this quarter to strongly drive the hardware sales".
In the three months ended June 30, Wii U software sales came in at just over one million, taking lifetime software sales for the console to 14.44 million. That means the current Wii U attach rate is at about four games for each console - an encouraging sign, and one which suggests the Wii U install base is predominantly core gamers.
Despite the poor unit sales, Nintendo's financial performance was more encouraging.
First quarter net sales rose 3.8 per cent year-on-year to 81.5 billion yen (£546m / $832m), while the company swung from a loss of 17.2 billion yen (£115 / $175) for the same period last year to a net profit at 8.6 billion yen (£57m / $88m).
Nintendo reported a first quarter operating loss of 4.9 billion yen (£33m / $50m) due to increased advertising and promotion of 3DS overseas and research and development for Wii U software.
3DS shone brightest for Nintendo, selling 1.4 million units and just over 11 million software units in the quarter, taking lifetime hardware sales to just under 32.5 million and software sales to just over 106 million.
Meanwhile, Wii sales of 210,000 units helped push the ageing system past 100 million lifetime sales. 3.67 million Wii games were also sold in the first quarter, meaning almost 873 million Wii titles have now been sold since the system launched in November 2006.
Nintendo's Wii U and 3DS sales forecasts for the full financial year ending March 31, 2014 remain unchanged from its previous guidance. The firm expects to sell nine million Wii U hardware units and 38 million Wii U games during the period, as well as 18 million 3DS units and 80 million games for the handheld.
On Monday, UK retail chain Asda announced it has suspended its Wii U stock.