"Income tax" means taxes levied regarding his/her earnings amount as the basis for the taxation. The Income Tax is one of the most major taxes imposed on Individuals all over the world. It is true in Japan, too.
Japanese Income Tax is levied when you and/or your earnings are strongly connected with Japan.
If you want to know about Japanese taxes on Individuals, you have to check at first the classification of persons and earnings for the tax purpose.
The treatment for the Japanese taxation on individuals is consistent no matter what nationality the tax payer has, in principle. Instead, Indivuduals are classified into following 3 categories according to their residential status. "PERMANENT RESIDENTS" and "NON-PERMANENT RESIDENTS" are called generically "RESIDENTS(KYOJYU-SHA)".
If you have a domicile in Japan and/or you have resided continuously in Japan for 1 year or longer, you are a RESIDENT.
If not, you are a NON-RESIDENT.
Provided you are a RESIDENT, if you meet 1 or 2 of the requirements below, you are a PERMANENT RESIDENT.
If neither, you are a NON-PERMANENT RESIDENT.
You are a Japanese national.
You have a domicile or residence in Japan for an aggregate period of 5years or longer within the last 10 years.
In accordance with your residential status I mentioned above, the taxable scope varies.
This table shows the taxable scope for tax payers of the each category.
The preceding paragraph is described simply based on the Japanese laws and Ordinances. However, we actually need to take Tax Treaties into consideration.
Japan concludes Tax treaties with many countries. These treaties do not increase your Japanese tax burden except for very few cases. Particularly as to a NON-RESIDENT, the Japanese tax burden may decrease by them.
Some tax treaties make a certain type of income gotten by a certain kind of people tax-free, in spite of the rule of Japanese income tax law.
For example, those who are from China and present in Japan solely for the purpose of study shall not be required to pay income tax on his/her revenues received for the purpose of his/her maintenance or education. It is due to article 21 of the tax treaty between Japan and China. That is to say, students from China, who earn employment income to the extent of amount corresponding to their living cost, are exempt from paying income tax.The tax treaty between Japan and Korea has a similar article under some additional requirement.
However, I am sorry that very few people know well about tax treaties. Further more, I cannot deny even some of tax office's staff or CPTAs may not know them precisely.
So if you are supposed to be exempt from paying tax by a tax treaty, it is not easy for you to apply for the treatment. I may tell it is near-impossible to make the arrangement by your own(unless you are very good at Japanese and with a lot of knowledge about international taxation).
If you are interested in special measures provided in tax treaties, I recommend you to consult a CPTA familiar to international taxation. You have to point plainly the measures you intend to apply for.