Regional health officials on Tuesday said a supermarket in the central city of Gamagori sold five packages of assorted blowfish meat.
The preparation of the fish must be meticulous, as the smallest mistake could result in the death of the diner.
The fish, known as fugu, is an expensive winter delicacy but requires a license to prepare because of the dangers of mishandling.
Local official Koji Takayanagi told AFP that a warning not to eat locally purchased fugu had sounded over speakers installed citywide using Gamagori's "emergency wireless system".
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Three of these have been located, and no one has yet been harmed, but two remain missing. One fugu could kill up to 30 people and there is no known antidote. The level of paralysis caused by the poison increases gradually, which leads to death within six to 24 hours.
With relation to diagnosis, the report said there is no particular antitoxin to combat the poison and treatment is supportive.
"Health authorities found that the store had been selling the liver of the particular kind of blowfish, called 'yorito fugu, ' or blunthead puffer, for years because it's almost non-toxic, health ministry official Yohei Ohashi said".
There is a collaboration between USA and the Japanese Ministry of Health and Welfare, which assures the fugu fish imported to the country are processed efficiently and certified safe for consumption.