Summary
If you make 5,989,116 円 a year living in Japan, you will be taxed 1,471,394 円. That means that your net pay will be 4,517,722 円 per year, or 376,477 円 per month. Your average tax rate is 24.6% 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.