Way before the release, the Chief Cabinet Secretary for Japan, Yoshihide Suga, came out saying that players of the game had to exercise caution and play the game in a safe manner.
The game is a major coup for Nintendo and could be the start of a turnaround for the struggling company.
Prior to the warning, markets had cheered the app's global success as a great sign for Nintendo's long-awaited move into the mobile games market.
It's likely that if Niantic's sponsored location system is successful - and it probably will be - we'll see a similar sponsorship deal in other regions Pokemon Go is available in, possibly even with McDonalds.
Nintendo added that it had taken the "current situation into consideration", but had decided not to upgrade its financial forecast.
Pokemon Go has captivated fans around the world, with 21 million active U.S. users in under two weeks of its launch. In those instances, perpetrators are using the opportunity to rob players.
"Everyone has been waiting for this", said Hideki Yasuda, an analyst at Ace Research Institute.
"There has been a view that Nintendo can not succeed in the smartphone business".
The company's stock fell 17.7% by the close of the Nikkei Index, roughly calculating to ¥5000 with Reuters reporting that this is the worst hit to Nintendo's share prices since October 1990.
McDonald's Japan shares rose around three percent following the announcement.
The smartphone app has now been launched in more than 40 countries, including the USA and much of Europe, but Japan - where Nintendo started the mythical creature franchise 20 years ago - was kept waiting. This, of course, seems to be a result of the increased string of incidents and crimes that players have been subject to since Pokemon GO launched.
Others are reminders of things that the typical player might not think about. With this, they have issued a flier with public safety tips.