Looking for more recent information, I find these news articles:
Japan Enhances Support for Pregnant High School Girls
Tokyo, April 15 (Jiji Press)--The Japanese education ministry has been enhancing support for pregnant high school girls, as its recent survey showed that 2,098 pregnant students were recognized at public high schools across Japan in fiscal 2015 and 2016.
The ministry recently instructed the education boards of prefectures and major cities to allow pregnant students not to perform in school gym classes if they submit related reports or participate in the classes as observers, officials said.
The ministry also asked the education boards to provide mental health care and other support measures to pregnant students while consulting with them and their parents.
The instructions also called for support for women who quit high school due to pregnancy, such as providing information on measures to cover school fees if they hope to return to school.
A suprapartisan group of lawmakers on the issue of child poverty had urged the government to take measures for pregnant high school girls, given that high school dropouts tend to face difficulties finding jobs.
On the other hand:
High schools told 32 teenage moms to ‘voluntarily drop out’
The education ministry is taking more action after learning that 32 female students at public high schools dropped out due to pregnancy or childbirth after being advised to do so in fiscal 2015 and 2016.
In some cases, schools urged them to drop out despite the fact that students were willing to continue their education or take a leave of absence. There is a concern that some may have ended up leaving school against their will.
The education ministry revealed the findings of the first-ever survey on the relationship between dropouts and pregnancy at Japanese public high schools.
“It is a concern, as being excluded from obtaining a high school education may lead to a cycle of poverty,” said a ministry official in charge of the survey. “We would like to ask schools to stop simply giving recommendations to leave, and instead give consideration for the students' sake.”
The ministry will notify education boards across Japan to give more consideration to the situation of the students.
According to the survey, 2,098 cases of students’ pregnancy or childbirth were recorded by high schools in fiscal 2015 and 2016.
After becoming pregnant, of the total, 371 students at full-time high schools, or 36.9 percent, and 271 students attending part-time schools, or 24.8 percent, left school “voluntarily based on either the students’ or their guardians’ will.”
There were no students who were expelled as a disciplinary measure over their pregnancies. However, 21 from full-time schools and 11 from part-time schools dropped out “voluntarily” after being advised to do so by their schools.
Anyway, it feels to me like a recent development and my waifu probably knows how things were in the olden days.
According to Unicef, Japan has the lowest teen pregnancy fertility rate in the world:
4 per 1000 (it's 64 in the US, 16 times higher).
Which probably is a reflection of a cultural difference and not just chance. (the pregnancy rate and the fertility rate are not the same thing, so I corrected that)