If you make 12,000,000 円 a year living in Japan, you will be taxed 3,765,900 円. That means that your net pay will be 8,234,100 円 per year, or 686,175 円 per month. Your average tax rate is 31.4% and your marginal tax rate is 38.2%. 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 38.24 円, hence, your net pay will only increase by 61.76 円.
A 1,000 円 bonus will generate an extra 618 円 of net incomes. A 5,000 円 bonus will generate an extra 3,088 円 of net incomes.