Nintendo shares dropped by 17.7% after they more than doubled in value since the game's launch on 6 July.
Pokemon Go was developed by US firm Niantic and Nintendo said profits from licensing and fees would be limited.
However, even with the decline, Nintendo shares are still up 60% since the release of Pokemon Go on 6 July.
Overall, Japanese shares were little moved, with the Nikkei 225 finishing flat at 16,620.29.
Nintendo said the accounting scheme for recognising revenues from Pokemon Go meant its profits would not materially change.
The sharp drop was the biggest decline since October 1990, leaving the stock down by 5,000 yen - the maximum daily limit allowed.
The gaming company is due to report first-quarter results this week and said it did not plan to revise its earnings outlook for now.
"Taking the current situation into consideration, the company is not modifying the consolidated financial forecast for now," Nintendo said in a stock filing.
However, some analysts believe the market "overreacted" to the Nintendo statement.
"I believe that Pokemon Go will be material in the company's earnings, given the current trends for the game," David Gibson, a senior analyst at Macquarie Securities Group said.
In China, Hong Kong's Hang Seng fell slightly by 0.07% to close at 21,948.94 while the Shanghai Composite traded flat most of the day and closed at 2,019.81 points.
In South Korea, the benchmark Kospi was also flat, closing at 2,012.32.
Australia's ASX/200 rose by 0.6% to finish at 5,533.60 points.
Star performer was Woolworth, with an 8% boost, after the supermarket chain announced it would close stores and cut staff numbers.
Shares in Nintendo have fallen sharply after the Japanese gaming giant said Pokemon Go's success would have a limited impact on its profits.