Summary
If you make 16,579,728 円 a year living in Japan, you will be taxed 5,065,930 円. That means that your net pay will be 11,513,798 円 per year, or 959,483 円 per month. Your average tax rate is 30.6% and your marginal tax rate is 38.4%. 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 38.42 円, hence, your net pay will only increase by 61.58 円.
Bonus Example
A 1,000 円 bonus will generate an extra 616 円 of net incomes. A 5,000 円 bonus will generate an extra 3,079 円 of net incomes.