The move is seen as part of the government's plan to tackle teen "sex delinquency".
A new 105-page manual, compiled with the help of teachers, the police and legal experts, has been distributed to all schools from kindergarten upwards. It tackles recent social problems including schoolgirl prostitution.
The redefined sex education - once taught under "purity education" - stresses the importance of respect for the opposite sex.
Despite Japan's sexually active student population there is no teaching about the newly available contraceptive pill, which is not prescribed to under-20s.