Summary
If you make 640,991,260 円 a year living in Japan, you will be taxed 291,475,578 円. That means that your net pay will be 349,515,682 円 per year, or 29,126,307 円 per month. Your average tax rate is 45.5% and your marginal tax rate is 46.1%. This marginal tax rate means that your immediate additional income will be taxed at this rate. For instance, an increase of 100 円 in your salary will be taxed 46.11 円, hence, your net pay will only increase by 53.89 円.
Bonus Example
A 1,000 円 bonus will generate an extra 539 円 of net incomes. A 5,000 円 bonus will generate an extra 2,695 円 of net incomes.