Well, bluntly put under Labor Law you owe them only 2 weeks. Company might say you need something else -- that's a total farce. This isn't a country where slavery is legal, despite what some forum members will tell you. You're allowed to put in written notice and then resign. Keep in mind that makes collecting unemployment much harder.
"One side cannot unilaterally terminate the contract without urgent cause. Urgent causes are the ones that I have mentioned. Likewise, the employer cannot choose to fire the one-year contracted employee unless there is sufficient cause. "
No offense but I don't think that's right. The Labor Standards law says that all workers are covered by the act. Anyone is allowed to resign whenever they want. The contract can say whatever it wants, but it's trumped by national labor law ultimately..
OP my friend resigned from GABA and got a lot of flack about not "being allowed to". You own your VISA, unlike Korea. They cannot cancel it. They cannot deport you, as they are not immigration. They cannot make you work there either, and you only owe them a legal 2 weeks notice.
I recommend you contact the General Union if you need professional advice. There are also labor attorneys in Tokyo that offer free advice. Don't let your work intimidate you. Ultimately they may feint you, but you're allowed to quit whenever you want, for whatever reason you want. I recommend leaving on good terms if possible, but don't let them muscle you either