Before you start

My Number
Address registration
Employment records or business accounts
A determination of your residence status for tax purposes

Step-by-step

1
Understand the three tax residence categories
A non-resident is taxed only on Japanese-source income. A non-permanent resident — broadly, someone without Japanese domicile resident five years or less in the past decade — is taxed on Japanese income plus foreign income remitted to Japan. A permanent resident for tax purposes is taxed on worldwide income.
OnlineWho: You
2
Let the year-end adjustment handle it if you are a straightforward employee
Employers run nenmatsu chōsei in December, reconciling the year's withholding against what you owe. Most employees never file a return at all.
Via employerWho: YouDecember
3
File a return if you are self-employed, on a research grant, or have foreign income
The filing season runs mid-February to mid-March for the previous calendar year. The blue return system gives a meaningful deduction in exchange for proper double-entry bookkeeping, which is worth setting up in month one.
OnlineWho: YouFebruary–March
4
Budget for residence tax arriving in your second year
Jūminzei is assessed on the previous calendar year's income and billed from June. Your first year in Japan produces almost none. Your second year is the real number and it arrives as a step change on the same salary.
OnlineWho: You
5
Know what the Nagasaki bill is made of
The per-capita portion from FY2024 is ¥3,000 to Nagasaki City plus ¥1,500 to Nagasaki Prefecture — of which ¥500 is the ながさき森林環境税 forest levy — plus ¥1,000 for the national Forest Environment Tax, so ¥5,500 a year regardless of income. The income-based portion is 10% of last year's taxable income, divided 6% city and 4% prefecture because Nagasaki is a core city rather than an ordinance-designated one.
OnlineWho: YouBilled from June
6
Appoint a tax representative before leaving Japan
If you leave partway through a year you may still owe residence tax on income already earned. Appointing a tax representative in Japan before you go is the clean solution; leaving without one creates a debt that is very difficult to settle from abroad.
In personWho: YouBefore departure

Documents you’ll need

My Number
Gensen chōshūhyō — the annual withholding statement from your employer
Business accounts, for the self-employed
Records of any foreign income and overseas assets
Deduction certificates for insurance, mortgage or dependants

Things most newcomers don’t know

Nagasaki splits the income-based residence tax 6/4, not 8/2, because it is a core city.

The income-based residence tax is 10% of taxable income everywhere in Japan. In ordinance-designated cities it has been divided 8% municipal / 2% prefectural since FY2018, when responsibility for teachers' salaries transferred to those cities. Nagasaki is a 中核市, so it keeps the standard 6% / 4% division. Your total is identical; the notice looks different, and an explanation written for Fukuoka or Hiroshima will not reconcile against it line by line.

Source: Nagasaki City

Nagasaki's per-capita floor is ¥5,500, and ¥500 of it is a levy on forests.

The flat portion everyone pays regardless of income is ¥3,000 city, ¥1,500 prefecture and ¥1,000 national Forest Environment Tax. The prefectural ¥1,500 is above the ¥1,000 standard because Nagasaki adds the ながさき森林環境税, a per-capita surcharge for forest conservation currently legislated through FY2026 — so check whether it has been extended before assuming the figure holds. It is small money, but it is the line on a first bill that people cannot otherwise account for.

Source: Nagasaki City; Nagasaki Prefecture

Residence tax is billed a year in arrears, which produces a second-year shock and an exit trap.

Jūminzei is calculated on the previous calendar year's income and collected from the following June. Arrive and your first year is nearly free of it; your second carries the full amount for your first year's earnings. Worse, if you leave Japan you can still owe residence tax on income already earned and spent. Settle it or appoint a tax representative before going.

Source: National Tax Agency

Furusato nōzei is unusually easy to justify from here.

The hometown tax donation scheme lets residents donate to a municipality of their choice, deduct almost all of it against residence and income tax, and receive a return gift worth a meaningful fraction of the donation. It is entirely legitimate, widely used by Japanese residents and almost unknown among foreign ones. Nagasaki Prefecture's island and coastal municipalities are among the more popular destinations nationally, and their return gifts are fish — which for a resident of this prefecture is a reasonable place to send it.

Source: Ministry of Internal Affairs and Communications

Common mistakes to avoid

Budgeting from your first year, when residence tax is almost nil.
Reading a designated-city explanation of the 8%/2% split against a Nagasaki 6%/4% bill and concluding something is wrong.
Assuming the prefectural forest levy is permanent — it is legislated to a fixed end year and periodically renewed.
Leaving Japan without settling residence tax or appointing a tax representative.
Never using furusato nōzei despite paying residence tax every year.

Some of this may be out of date. Spotted something inaccurate? Help us keep it right for the next newcomer.