Catching Up on Unfiled Japan Tax Returns: A Step-by-Step Checklist for Americans

【Koshida Accounting Firm Column Date:】

My name is Taisei Koshida. I am a Japanese certified public accountant and tax accountant, and I help Americans and other foreign residents with their Japanese tax returns in English.

Some of the Americans who contact us have not filed their Japanese tax returns (kakutei shinkoku) for one or more years. This article sets out the steps for filing late tax returns (kigen-go shinkoku) and paying back taxes in Japan, based on how we handle these cases in practice.

For the background, see What Happens If You Don’t File Taxes in Japan? and The Penalty for Filing Late Tax Returns in Japan.

Step 1: Consult a Tax Accountant Before Contacting the Japanese Tax Office

Before contacting the tax office, it is useful to know which years need to be filed, the approximate amount of tax, additional tax and late-payment interest, and how the tax will be paid. A tax accountant can work this out with you. With these figures in hand, you can plan the order of filing and the payment.

Timing also matters. A late return filed voluntarily before the tax office gives notice of an audit is subject to lighter additional tax than one filed after the notice. For that reason, the review and the filing should not be left for long.

Step 2: Confirm Which Years of Japanese Tax Returns Need to Be Filed

For each year, check:

  • Your residence status for Japanese tax purposes, and whether you were a non-permanent resident (a non-Japanese resident who has lived in Japan for five years or less in the past ten years). This determines how your U.S. income is taxed. See How to Calculate the Non-Permanent Resident Period in Japan.
  • Whether you had income that requires a return, such as business income, rental income, U.S. investment income, or salary from two or more employers.

The tax office can generally assess tax for five years from the filing deadline, or seven years where there was deception or fraud. In practice, we start with the most recent five years. See Tax Statute of Limitations in Japan.

Step 3: Gather Documents for Each Year

  • Japanese withholding slips (gensen choshu-hyo) from each employer
  • W-2s, 1099s, brokerage statements, and RSU or stock option statements
  • Rental income and expense records
  • Bank statements in Japan and the U.S.
  • Receipts and records for business income and expenses

Missing records are common. In that case, we reconstruct income and expenses from bank statements and other available evidence.

Step 4: Plan How to Pay the Back Taxes

Late-payment interest continues until the tax is paid in full. Unpaid tax is also relevant to visa applications.

Unpaid Tax, Visa Renewal and Permanent Residency in Japan

A visa renewal application usually includes resident tax (juminzei) certificates from your city office, which show your income and payment status. When you file late income tax returns, the city office also assesses resident tax for those years. Any unpaid amount appears on the certificate.

Under the Immigration Services Agency’s renewal guidelines, failure to pay tax is a negative factor, and large or long-term unpaid amounts are treated as serious. The guidelines also note that the Agency can refer to information on tax payments provided by other public bodies. The permanent residency guidelines are stricter: tax not paid by the original due date is, in principle, evaluated negatively even if it has been paid by the time of the application.

Paying Back Taxes in Installments

Payment in installments is possible under a deferral. For a late return, the tax is due on the date of filing, so the payment plan should be prepared before filing.

  • Tax on a return filed more than one year after the original deadline: a payment deferral can be requested by the due date if the tax cannot be paid in a lump sum.
  • Other cases: a deferral of enforcement can be requested within six months of the due date, provided there is no other unpaid national tax and the taxpayer intends to pay in good faith.
  • In both cases, the deferral period is generally up to one year.

During a deferral, the tax remains unpaid. According to the National Tax Agency, the tax payment certificate (nozei shomeisho) No. 1 states the unpaid amount and that it is under deferral, and Certificate No. 3 (no unpaid tax) is not issued for that tax.

A permanent residency application requires Certificate No. 3 for income tax, consumption tax, inheritance tax and gift tax. While installments are ongoing, this certificate is not available.

In practice, we recommend:

  • completing the filing and payment before the next visa renewal or permanent residency application;
  • where installments are needed, arranging them early and keeping the approval and payment records, so that the situation can be explained in the application. The decision itself rests with immigration;
  • consulting an immigration lawyer or gyoseishoshi on the visa side. We handle the tax side and coordinate with them.

Step 5: If You Have Already Left Japan

Tax for the years you lived in Japan still needs to be filed and paid after you leave. A non-resident generally needs to appoint a tax representative (nozei kanrinin) in Japan to receive tax documents and make payments. See Who Needs to File a Japanese Tax Return After Leaving Japan?

Step 6: Coordinate With Your U.S. Return

U.S. citizens also file U.S. returns. Japanese tax paid for past years affects the U.S. return, for example through the foreign tax credit. We prepare the Japanese side and provide the Japanese figures to your U.S. tax preparer.

How We Can Help

  1. First consultation: free for up to 20 minutes, or up to two replies by email. We identify which years are likely to be affected.
  2. Estimate: we estimate the tax and our fees. Individual tax returns start from approx. JPY 100,000 per year (plus consumption tax). For multiple years, we quote after reviewing your documents.
  3. Filing and payment plan: we prepare the returns and plan the payment around your visa schedule.

We usually reply within 3 business days (from February to April, it can take about a week). Please feel free to contact us through the inquiry form.

Frequently Asked Questions

Should I contact the tax office first to show good faith?

We recommend consulting a tax accountant first, so that you know the amounts and have a plan. Filing promptly after that is what matters.

Can I renew my visa or apply for permanent residency if I owe back taxes in Japan?

Unpaid tax appears on the certificates submitted with a visa application and is a negative factor in the review. During installments, the certificate of no unpaid tax required for permanent residency is not issued.

Do I need to file for years more than five years ago?

Generally, the tax office cannot assess tax more than five years after the deadline. Where there was deception or fraud, the period is seven years. Which years to file depends on the facts.

Sources

The following official sources (in Japanese) were checked in November 2026.

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This article is general information, not advice for a specific situation. Tax law and immigration practice are subject to change.

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