Even if the incidents are egregious, this is not even among the top twenty reasons that "many" refuse to attend.
As far back as the 1980's it was widely reported that Japanese expectations for children's performance and good behavior drive them to mental illness, from the top down, starting with the demands of parents.
I just have anecdotal evidence. The two kids I know here who regularly skipped school did so because of racist bullying. And yes, hearing "that's your fault because you are a minority" is indicative of a mentality that does not want to fix the problems of people who don't "fit in the mold".
"As far back as the 1980's it was widely reported that Japanese expectations for children's performance and good behavior drive them to mental illness"
Yes, "good behavior". "Why can't you be like the others?" "Why are you the cause of trouble?" Repeat that every day to any normal kid and they won't want to go to school.
Perhaps racism isn't the right descriptor.
Japan has a caste system that puts India's to shame. It's smaller in the number of people living in the lower tiers, but the effects are amplified to a high degree.
At least India puts some effort, futile or not, into forcing representation for its untouchables.
In Japan, a member of the untouchable caste is actual, literal, human garbage especially in the western parts of the country.
It is illegal for parents to investigate the background of their children's potential marriage partners in order to determine if they are a member of an untouchable caste.
Investigations still occur regularly.
Anyone who claims that it is not still a problem is either lying, or is a Japan-obsessed foreigner whose impressions of the country are based on a weeklong trip to Tokyo.
I'm willing to bet that many of the children refusing to go to school are those with the "wrong" family name.
However I heard of two marriages kind of broken by parents who did not want a foreigner in their ranks though.
Racism does exist and I witnessed several occurrences of it against black people. Whites are generally better received, especially French, like I.
Racism and discrimination aren't just reserved to the color of skin, it's often built around whole ancestries of groups and their traditional social standings [0].
For the same reason, the Nazis killed people that were just as white as themselves, as most scientific racism [1] went way past defining races merely by the color of skin [2] and anti-Slav sentiments are something very present in many Western European countries to this day.
Case in point: The Nazis, and many other white-supremacists, consider themselves to be Aryans, supposedly descendants of the lost continent of Atlantis [3] and apparently the top of their imagined race pyramid.
[0] https://en.wikipedia.org/wiki/Burakumin
[1] https://en.wikipedia.org/wiki/Scientific_racism
[2] https://en.wikipedia.org/wiki/Untermensch#Etymology
[3] https://en.wikipedia.org/wiki/Aryan#Nazism_and_white_suprema...
Indeed, but this exists everywhere. Why would this factor be unusually influential in Japan?
Case in point: Japan has "family rental services" [0] for those people that spend too much time working, thus lacking the time to maintain an actual family. Which is the result of societal expectations along the lines of "A successful businessman also has a successful family". When in reality most struggle to just support themselves, the idea that a single earner can feed a whole household is something that also hasn't applied in Japan for a while anymore.
Hikikomori [1] are another, much earlier recognized manifestation of this, that even has somewhat of an equivalent with Western countries "NEETs". The reasons for those are not singular, they are as multifaceted as most social problems are. Racial and class discrimination plays just as much of a factor as the economic downturn, leaving most young Japanese, like young people in many other countries, without much of any perspective.
Here’s the Wikipedia article.[0] Japanese (the nation) citizens of non-Japanese (the ethnic group)[1] suffer discrimination, particularly the indigenous peoples (the Ainu just got formal recognition a decade ago) and people of backgrounds Japan (the nation) has had historical enmity with (Chinese, Korean).
Whether or not we can parse specifically what portion of kids not wanting to go to school is due to this, the fact that 30% of non-Japanese ethnicity respondents of a poll conducted by the Justice Ministry said they had experienced hate speech and 40% said they had faced housing discrimination[2] seems like it would absolutely have an impact on the school experiences of those children.
This is all limited to the types of racism that are pervasive in Japanese society that a broad portion of the student population may have experienced, but Japan’s particularly strong anti-black sentiment is also notable when discussing racism in Japan more broadly.
As to why this might be a particularly strong factor in Japan, as opposed to being some sort of “cosmic background racism” present everywhere, Japanese people’s self-conception of Japan is very tied up in ethnic identity in a somewhat unique way (maybe the prevailing sentiment of Jewish people living in Israel is somewhat similar).[3] Government officials used to talk openly about one culture, one race—when Japan has never really been that and is becoming less so with time. 10% of Tokyo is foreign born, to say nothing of those who were born in Japan of non-Japanese ancestry.
[0] https://en.wikipedia.org/wiki/Ethnic_issues_in_Japan [1] https://en.wikipedia.org/wiki/Yamato_people [2] https://www.japantimes.co.jp/opinion/2018/06/03/commentary/j... [3] https://archive.ph/20070519010856/http://search.japantimes.c...
One datapoint, but I thought it was interesting.