In Japan, there are two kinds of taxes on individual income ; one is Income Tax for national taxes, the other is Resident Tax for local taxes.
More specifically resident tax is divided into municipal and prefectural resident taxes, but each city, town, or village office is in charge of taxing and collecting both of them.
日本で個人の所得に課税される税金には国税の所得税と地方税の住民税があります。
住民税には市民税と県民税がありますが、どちらも市町村が一括して課税徴収を行っています。
Resident tax must be paid by foreigners who have stayed in Japan for a year or more before New Year's Day or who plan to stay in Japan for a year or more after his or her arrival. The city, town, or village office where you live on New Year's Day is in charge of your resident tax for that year.
So in any case you don't have to pay resident tax the first year you are in Japan.
Most company-employed workers don't have to file their tax returns. If you have worked for only one company throughout the year, and have no income other than the salary from that company, there will be a tax adjustment at the end of the year according to your salary.
Then your company sends our office a document which shows the yearly amount of your salary, the number of your dependents, and other details necessary for the calculation of the resident tax.