Employment income can be subject to national income tax (所得税), withheld from each payslip, and local residence tax (住民税). Residence tax is assessed by the municipality where you are registered on 1 January, which is why the bill can arrive long after the income did.
Why the bill is late
Residence tax is generally assessed on income for the previous calendar year and collected from June through May of the following year. A new arrival often has little or no prior-year Japan-taxable income, so the first collection year may be low. That is a common pattern, not an exemption for every first-year resident.
The practical consequence is that take-home pay may fall when residence-tax collection starts, even on identical gross pay. The exact year and amount depend on arrival date, prior-year taxable income and how the municipality collects it.
The year-end adjustment
For most employees, income tax is settled by the year-end adjustment (年末調整) in November and December. Your employer reconciles what was withheld across the year against what you actually owed, and the difference appears in a December or January payslip.
You are asked for declarations and certificates around November — dependants, life and earthquake insurance premiums, and any national pension or health insurance you paid yourself. Certificates you do not hand in are deductions you do not get, and they arrive by post in October and November, which is exactly when they look like junk mail.
When you have to file yourself
The year-end adjustment does not cover everyone. The ordinary filing season is in mid-February to mid-March, but the National Tax Agency publishes the exact dates for each year. Common filing triggers for salary earners include:
- Your employment income was above ¥20 million
- You had one salary payer and more than ¥200,000 of income other than employment or retirement income
- You had multiple salary payers and the total of non-primary salary plus other non-employment/retirement income exceeded ¥200,000, subject to the statutory exceptions
You may also need or choose to file when no employer completed the year-end adjustment, to report tax-deductible private pension contributions (see NISA and iDeCo for foreigners), or to claim items such as medical expense tax deductions (Iryōhi Kōjo), a first-year housing-loan deduction, or donations not covered by the furusato nozei one-stop exception. Filing obligations and refund claims are not the same thing.
What changed in the 2025 reform
For 2025 and later income tax, the statutory basic deduction (基礎控除) became ¥580,000 for people within the main income limit, with temporary additions that make it as high as ¥950,000 in lower income bands. The minimum employment-income deduction also rose to ¥650,000.
The often-quoted “¥1.6 million threshold” describes a simple salary-only example at the low end, not a universal tax-free allowance. The basic deduction is tiered by total income, the temporary additions change over time, and residence-tax thresholds are separate. Confirm your own position with the National Tax Agency or your employer rather than a summary.
Furusato nozei, briefly
A furusato nozei (ふるさと納税) payment is legally a donation. To count for a calendar year it must be completed by 31 December. Within the applicable ceiling, deductions generally apply to the amount above a ¥2,000 self-burden through a tax return or the one-stop exception. Check out our in-depth walkthrough on how to do Furusato Nozei step-by-step. Your ceiling and procedure depend on your income and circumstances; any excess remains a donation.
Where to confirm this
- National Tax Agency filing guidance for salary earners
- National Tax Agency 2025 basic-deduction reform guidance
- Our step-by-step guide to Furusato Nozei
- Our guide to medical expense deductions
- Our guide to leaving Japan and residence tax
- Your city or ward office — residence tax, payment slips, and appointing a tax representative
Guides are dated rather than undated: last reviewed 13 September 2026. This is an organisational aid, not legal or immigration advice — always confirm anything consequential with your ward office, the Immigration Services Agency, or a qualified professional.