The Tokyo metropolitan government has cut teachers' pay and demoted the principal at a school for disabled pupils because it taught sex education.
It has ordered Nanao nursing school in Hino, western Tokyo, to stop teaching disabled children the facts of life and has confiscated sex education materials, including model penises.
As part of a conservative backlash against sex education in schools, the prime minister, Junichiro Koizumi, and his education minister, Nariaki Nakayama, have also threatened 80 Tokyo schools with unspecified action for using anatomically accurate dolls in their lessons.
They have pledged to crack down on "over-explicit" materials after pairs of "Suzy and Fred" dummies were introduced in the capital's elementary schools.
"Is it really necessary to show them this much?" the prime minister asked the Japanese parliament in a recent debate, as he waved copies of another controversial textbook for elementary students that was introduced recently in Osaka when teachers heard about the use of the dummies.
"This is all too explicit," he said.
According to social analysts, the Japanese attitude to sex education is "don't wake a sleeping baby".
The subject is not part of the national curriculum and the education ministry gives schools discretion about how much sex education they teach.
For most elementary schools, this has meant a maximum of an hour a year being devoted to what was known until recently as "purity studies".
Many schools leave out sex education entirely or avoid the mention of sexual intercourse, as advised by at least one manual published by Tokyo's board of education last year. Little is taught about contraception. Condoms are described, but there is no explanation about how they are used.
Official guidelines forbid the mention of birth-control pills for fear that it will "turn children promiscuous".
So the main sources of information on sex in Japan remain the rape scenes often featured in manga cartoon strips, the internet and hearsay.
At the same time, child prostitution is increasing and young people are becoming sexually active earlier. Rates of HIVAids are increasing.
Yukio Takegawa, the head of the Children's Sex Education Research Network, recently told Shukan Bunshun magazine: "We've reached the time when Japan's parents have to grow up a bit and confront sex-education issues face-to-face, like American parents do."