A 6-month-old boy in Adachi Ward, Tokyo, died late last month of infant botulism after his family fed him honey, according to the metropolitan government.
Metropolitan officials said it was the first death caused by infant botulism in Japan since 1986, when the government began compiling such statistics.
The officials warned that babies younger than 1 should not be given honey.
They said the Adachi boy died March 30. He developed a cough on Feb. 16, and was taken to a hospital by ambulance on Feb. 20 after going into convulsions and suffering respiratory failure. He was diagnosed Feb. 28 as having infant botulism.
The officials said the boy's family had been giving him honey mixed in juice twice a day for about a month, and that they were not aware babies should not be fed honey.
The bacteria Clostridium botulinum was found in an unsealed honey container in the family's house and in the boy's excrement. A public health center confirmed that the boy's death was caused by botulism poisoning.
Infant botulism can occur when newborns, who have immature digestive systems, ingest bacteria that produces toxins inside the bowels.
According to the health ministry, Japan's first recorded case of the disease was confirmed in Chiba Prefecture in 1986 and the ministry issued a warning the following year to prefectures nationwide not to feed honey to babies.
According to the Tokyo Metropolitan Government, more than 30 cases of infant botulism had been reported nationwide since 1986, but none were fatal.
Botulism poisoning is caused by honey in most cases, but there have been cases in which it was caused by vegetable soup or well water, experts say.