The five packets of fugu that triggered the alarm in Gamagori were sold with their livers still in place, Agence France-Presse reports.
The fish, known as fugu, is an expensive winter delicacy but requires a license to prepare because of the dangers of mishandling.
"Three packages will be retrieved today, but we still don't know where the remaining two are".
Local officials have warned the population not to eat blowfish until the missing portions are recovered.
It is usually served raw or in a soup. Tetrodotoxin poison will cause numbness around the mouth, then paralysis and that can lead to a person's death.
"Eating a blowfish liver can paralyse motor nerves, and in a serious case cause respiratory arrest leading to death", regional officials said in a warning statement.
The Fugu fish is a delicacy, but before it is eaten, the livers must be removed as they contain a potentially deadly poison, which is 1,200 times more lethal than cyanide.
In comparison, around 100 people die in the United States every year from vibrosis, which is a disease linked to the eating of raw oysters and shellfish.
A fugu fish on a chopping board for the removal of toxic internal organs.
However, the Telegraph reported that more traditional chefs were shunning the safer breed as customers preferred playing Russian roulette with their meals.
Several people in the country are killed each year because of the incorrect way or rashly trying to cook the fish.
"Where is the enjoyment in eating something that has no risk in it?"