Actually, if you work for a company in Japan, you don't need to worry about taxation at all.
They usually withdraw income tax"shotokuzei", health insurance "kenko-hoken" and pension"nenkin" premiums from your monthly salary. At the end of the fiscal year, the company will do the tax return thing, like calculation and filing, for you.
The percentage of taxation differs depending on how much you earn. It should be less than 30%, but I don't know exactly.
Life insurance premium and mortgage interest are tax deductible.