Summary
If you make 3,413,340 円 a year living in Japan, you will be taxed 689,372 円. That means that your net pay will be 2,723,968 円 per year, or 226,997 円 per month. Your average tax rate is 20.2% and your marginal tax rate is 23.1%. 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 23.12 円, hence, your net pay will only increase by 76.88 円.
Bonus Example
A 1,000 円 bonus will generate an extra 769 円 of net incomes. A 5,000 円 bonus will generate an extra 3,844 円 of net incomes.