Read SubaHibi. It takes real bullying accounts in Japan to its story. The bullying in Japan is fucked up! I mean Junko Furuta is just the tip of the iceberg.
It's prevalent in adult society too. Professional sumo and workplace conditions that led to people dying... Japan is fucked up!
As if similarly despicable things don't happen elsewhere. Kids in schools all around the world are stressed beyond their limits, exposed to untrustworthy adults, bullied by peers, even trafficked or shot. At least Japanese kids don't get shot.
You're only singling out Japan because it has a highly overactive creative and media industry that thrives on drama and has a fascination with school life. As well as an overeager western cadre of western journalists and academia who like to use Japan in particular to engage in social projection about social evils. Since Japan has a mature first world society and Japanese are too starry-eyed about the west to realize they are often lampooned or deconstructed by them, unlike say Koreans or Chinese.
All you know about Japan likely comes from stylized or cherrypicked sources, if you're going to use something like Subahibi as your supporting evidence.
Historically, Japan has had a higher suicide rate among young people (under 24) than say the USA by around 20~30%. But in recent years this has fallen and is about 1/3rd that of the US. Suicide rates still remain slightly high versus the world average and is rising again, but this is being attributed more to economic hardship and those on the older side of that band, i.e. entering the workforce, a common trending theme across the developed world.
There are lots of problematic social issues in Japan from my own experience. And that includes schools. But it is neither particularly special nor is it the worst, especially compared to many Asian countries. But what am I talking about. You have such impeccable sources as visual novels or manga, there's no way I can compete with you.
For everyone else. Well...yeah, unfortunately, when bullying happens in Japanese (or tbh, most Asian schools), it's often not dealt with. Not many students will admit to being bullied for starters. And teachers often don't want to get involved, because they can be seen as complicit if it went undetected for some time by parents and authorities. But it's also true the manga is quite unrealistic. Bullying is usually a lot more subtle than beat-ups...or at least ones that leave lasting injuries.
If you want to actually finger something specific to bullying in Japanese schools, there are a lot of ways to put pressure on targets without ever touching them thanks to how easily social stigma can be cultivated. This is 2025, not the showa era. Today there's no chance teachers or guardians will ignore or miss physical injuries or do nothing about such obvious results of bullying. Just don't forget you're reading manga.