Summary
If you make 6,408,576 円 a year living in Japan, you will be taxed 1,605,016 円. That means that your net pay will be 4,803,560 円 per year, or 400,297 円 per month. Your average tax rate is 25.0% and your marginal tax rate is 31.9%. 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 31.86 円, hence, your net pay will only increase by 68.14 円.
Bonus Example
A 1,000 円 bonus will generate an extra 681 円 of net incomes. A 5,000 円 bonus will generate an extra 3,407 円 of net incomes.