The Japanese Health Ministry is calling for a nationwide suspension of the Japanese encephalitis vaccination paid for by local governments following a report of serious side effects caused by the shots.
Until a safer vaccine becomes available for the potentially fatal encephalitis, a disease that causes inflammation of the brain, the ministry is urging all local governments not to recommend the vaccination to minors.
A new vaccine which is being developed is being produced by a tissue-culture method that reduces the risks of side effects, but will not be available until next year.
This move by the Ministry of Health, Labor and Welfare follows the news that a high school student in Kai, Yamanashi, developed acute disseminated encephalomyelitis.
The student was given the vaccination in July last year, but became critically ill with breathing difficulties and other problems and remains hospitalized.
An investigative report by the Kai City Government in March this year says the girl's condition was apparently caused by side effects from the vaccination.
The ministry's sickness and disability certification council in response to the report, last week conceded the vaccine was a potential health hazard.
Parents can however still choose to have their children inoculated with the publicly funded vaccine.
Japanese encephalitis is transmitted to humans from pigs through mosquitoes and can cause high fevers, headaches and even death.
The annual number of encephalitis patients in Japan exceeded 1,000 before 1966. However, there have been only a handful of such cases every year since 1992 with improvements to mosquito-extermination methods and other conditions.
Japanese children are usually given the vaccination three times: between 6 months and 7 years old, 9 and 12 years old, and 14 and 15 years old.
Between 4.2 million and 4.3 million children receive the encephalitis vaccine a year.