The Japanese gaming giant saw an operating loss of 19.6 billion yen ($258m / £161m) for the period between July to September, according to Reuters.
In comparison, Nintendo saw a profit of 30.9 billion yen ($407m / £254m) in the same period last year.
The worse than expected losses has meant that the company has shrunk its expected profit forecast for the 2011-2012 financial year from 35 billion yen to 1 billion yen.
While Nintendo 3DS software forecasts were lowered from 70m units to 50m, hardware predictions will remain the same at 16m units for the financial year.
The weak yen, poor software sales and ongoing competition from phone and handheld manufacturers such as Microsoft, Sony, Apple and Google have been to blame for the recent losses.
Nintendo's stock dropped by 12% when it announced the 3DS price cut earlier this year.
> Read our ongoing coverage of the Nintendo 3DS