Year-End Adjustment Wrong? How to Fix It (還付申告)

Quick Answer: It depends on when you notice. Until the end of January, your employer can redo the adjustment if you hand in the missing form. After that, you fix it yourself with a refund return (還付申告), which you can file for five years from 1 January after the tax year. The window for 2021 closes at the end of 2026.

Every December the year-end adjustment settles your tax for the year, and every January a lot of people find out it settled it wrongly: an insurance certificate that never got handed in, a dependant who was left off, an iDeCo certificate still in a drawer.

None of that is final. The fix just depends on the calendar, and on whether you have filed anything yourself. This guide covers how to spot the error, which of the three routes applies, and what happens to your resident tax afterwards. For the difference between the year-end adjustment and a tax return in the first place, start with 年末調整 vs 確定申告.

This is educational information, not tax advice. Confirm your own position with the National Tax Agency (NTA) or a qualified tax professional (税理士).

How do you know your 年末調整 was wrong?

Your employer gives you a 源泉徴収票 (withholding slip) for the year, usually with the last pay of December or in January. It is the only document that shows what the adjustment actually applied. Check it line by line against your own life:

Line on the 源泉徴収票 What to check Common miss
控除対象扶養親族の数 Number of dependants claimed A relative abroad whose documents weren't submitted — see overseas dependants
配偶者（特別）控除の額 Spouse deduction applied Partner's income estimate was wrong, in either direction
社会保険料等の金額 Pension, health and employment insurance, plus iDeCo iDeCo paid from your own bank account, with no certificate (小規模企業共済等掛金払込証明書) handed in
生命保険料の控除額 Life, medical and pension insurance Certificate arrived after the deadline, or a policy was left off — see the life insurance deduction
地震保険料の控除額 Earthquake insurance Same — the certificate is annual
住宅借入金等特別控除の額 Housing loan credit Blank in the first year is normal; that year always needs a return
源泉徴収税額 Tax actually withheld for the year If this is 0, there is nothing to refund

That last line matters more than it looks. The NTA is explicit that an income tax refund only exists where tax was already withheld: if the 源泉徴収税額 box reads zero, filing a return produces no income tax refund, however many deductions you add. Deductions can still lower your resident tax, which is calculated separately.

Some deductions are never on this slip because the adjustment cannot apply them at all: medical expenses, the first year of the housing loan credit, and donations including Furusato Nozei (One-Stop, where it applies, works outside the adjustment). Those are not errors; they always need a return. The year-end forms guide covers which form feeds which line.

What if you notice before the end of January?

Hand your employer the missing form. The NTA's own year-end adjustment handbook allows the employer to redo the adjustment up to the end of January of the following year, the point at which the 源泉徴収票 is finalised. The situations it lists include a late insurance deduction form, a housing loan deduction form submitted late, and a change in the number of dependants. The redo covers that year's facts only: premiums paid during the year, and dependants as they stood on 31 December. A change that happens in January belongs to the next tax year.

This is the easiest route by far: no return, no tax office, and the difference normally comes back through payroll. But the rule says the employer can redo it, not that it must, and payroll teams are busiest exactly then. If yours declines, nothing is lost; you simply move to the next route.

What if it's already February or later?

You file a 還付申告, a return made purely to reclaim tax that was over-withheld. It is not tied to the February–March filing season. In the NTA's words, it can be filed 「その年の翌年1月1日から5年間」: for five years, starting 1 January after the tax year.

So in September 2026, the years still open are 2021 to 2025:

Tax year Window opened Window closes
2021 1 Jan 2022 End of 2026
2022 1 Jan 2023 End of 2027
2023 1 Jan 2024 End of 2028
2024 1 Jan 2025 End of 2029
2025 1 Jan 2026 End of 2030

If a missed certificate, dependant or large medical year sits in 2021, the claim expires on 31 December 2026. The NTA treats the window as ending on 31 December, and tax offices close for the New Year holiday from 29 December, so don't leave it to the final week.

Each past year uses that year's rules. For 2021, a dependant's income limit was ¥480,000 (¥1,030,000 of salary), not the 2026 figures.

This route is for people who were not required to file. If you were (for example, salary over ¥20 million, or more than ¥200,000 of other income), a late return is a different matter; see 年末調整 vs 確定申告.

Four practical points:

A small exception worth knowing: some special provisions require a return by the normal 15 March deadline even when it is a refund. They mostly concern the self-employed (such as the blue-return special deduction), not the salaried errors above.

What if you already filed a return and it was wrong?

Then it isn't a 還付申告 any more; it is a correction, and the direction matters.

You under-claimed (too much tax, or too small a refund): file a 更正の請求, a request for correction. The tax office reviews it and, if it agrees, reduces the tax and refunds the difference. The window is generally five years from the statutory filing deadline. One wrinkle: if you were not required to file and the return you are correcting was a refund return, the NTA says the five years run from the date you filed it.

You over-claimed (too little tax, or too large a refund): file a 修正申告, an amended return. The NTA's guidance is to do it as soon as you notice. A voluntary correction made before the tax office gives notice of an examination carries no under-reporting penalty (過少申告加算税), though late-payment interest (延滞税) still runs to the date you pay.

Both forms can be prepared in the 確定申告書等作成コーナー.

What if the mistake was in your favour?

It happens more than people think: most often a spouse or relative claimed as a dependant who, it turns out, earned over the limit. For 2026 the dependant limit rose to ¥620,000 of income (¥1,360,000 of salary), so check against the right year's figure.

If you had no return of your own, the fix runs through the employer. The NTA tells employers that where dependants decrease, they should redo the adjustment and collect the shortfall, and that a redo which produces a shortfall must be done even after the end of January. Tell payroll rather than waiting for them to find it. If you did file a return, it is the 修正申告 route above.

What happens to your resident tax?

It follows automatically. When you file an income tax return, the information is passed to your city or ward, so you don't normally file a separate resident tax return. Chuo City in Tokyo states this directly.

Because resident tax is billed a year in arrears, a return for a past year usually changes a bill you have already been paying. The city recalculates, sends a revised assessment, and refunds any overpayment. Nakano City, for example, says it sends a tax change notice and a refund notice once processing finishes, which typically takes three to four months, and longer for past-year returns filed between February and June, when the ward is processing the current year. Procedures vary by municipality, so check with yours.

What should you gather before filing?

Then see what the refund does to your plan. Run the corrected year through the Japan salary tax calculator, and put your real take-home into the PlanTogetherFI calculator.

PlanTogetherFI is for educational planning only. It is not tax, legal or financial advice. Tax rules, deadlines and municipal procedures change and depend on your circumstances — confirm with the National Tax Agency, your city or ward office, or a qualified tax professional (税理士).

Frequently Asked Questions

Can my employer redo my year-end adjustment?

Yes, up to the end of January of the following year, if you submit the missing or corrected form. The NTA's handbook lists late insurance and housing loan deduction forms and changes in dependants among the cases. It is permitted rather than required where the change would increase your refund, so if your employer declines, you file a refund return yourself.

How far back can I claim a missed deduction in Japan?

Five years. A refund return (還付申告) can be filed from 1 January of the year after the tax year, for five years. In 2026 that covers the 2021 to 2025 tax years, and the window for 2021 closes on 31 December 2026. Each year is assessed under its own rules.

I forgot to submit my life insurance certificate. What do I do?

Before the end of January, give it to your employer and ask them to redo the adjustment. After that, file a refund return for that year with the certificate details and your 源泉徴収票. The same applies to earthquake insurance and to an iDeCo contribution certificate if you pay iDeCo from your own account.

Will fixing my income tax also fix my resident tax?

Normally yes. Your income tax return is passed to your city or ward office, which recalculates resident tax for the matching year and refunds any overpayment. Nakano City, for example, says this typically takes three to four months after you file.

I already filed a tax return and missed something. Is it too late?

No. File a request for correction (更正の請求), generally within five years of the statutory filing deadline, or within five years of the filing date if you were not required to file and your original return was a refund return. If you under-reported instead, file an amended return (修正申告) promptly.

What if I claimed a dependant who earned too much?

Tell your employer. Where dependants decrease, the NTA tells employers to redo the adjustment and collect the shortfall, and a redo that produces a shortfall must be done even after the end of January. If you filed your own return, correct it with an amended return (修正申告) as soon as you notice.

Sources and further reading

Rules reflect the position as of September 2026. Confirm your own case with the NTA or your municipality.