> That's more like 1.1 million yen / year.
Thanks. It's actually 1.03 million year in gross income. After applying the income exclusion, you end up with (1,030,000-650,000) = 380,000 JPY in net income.
> Dutch Baka
So you filled out your withholding tax form wrong, not including your children? But your employer withheld less each month because they assumed you were taking the deductions for your kids? But at the end of the year, they realized you didn't ask for the deduction for your kids, so you had to pay the money back?
If that's the case, just fill out a kakutei shinkoku before March. Fill in the proper details about your dependents, and include any medical costs above 100,000 JPY and any other personal business expenses you might have. You will get the money back again.
And right around now your employer should be asking you to fill in the withholding tax information for 2011. You will be able to include your spouse as a deduction for income tax, but as I mentioned above, children under 16 can only count as dependents for local taxes.