A net loss of 25.5bn yen for the April to June quarter, which is equivalent to $324m, £201m, was reported by the company compared with a loss of 25.2bn in the previous year.
Nintendo now expects a net income of 20bn yen, losing 82% from its previous estimate for the year to March 2012.
The cost of the 3DS console was slashed sharply in Japan and the US.
The price in Japan will be around 40% less-retailing at 15,000 yen. In the United States, the cost will go down next month to $169.99 from $249.99.
Reggie Fils-Aime, US president of Nintendo, said, “For anyone who was on the fence about buying a Nintendo 3DS, this is a huge motivation to buy now.”
The total sales throughout the quarter went down by over 50 percent to 93.33bn yen.
Around 80 percent of sales of Nintendo are from outside of Japan, meaning it has been hit harshly by a strong yen.
The shares of the company in Tokyo have decreased by over 40 percent this year.