Japan JCT Registration for Cross-Border Sellers: Qualified Invoice System, Thresholds and Compliance

Yes, if your taxable sales in Japan exceed ¥10 million in the base period, you must register for JCT. Amazon Japan requires sellers who are JCT-registered to display their registration number on listings. Since October 2023, the Qualified Invoice System makes JCT registration more important: if you are not registered, your business buyers cannot claim input tax credits on purchases from you, which may reduce your sales. Amazon Japan automatically collects and remits JCT on marketplace sales where Amazon is the deemed supplier, but you still need your own registration if you exceed the threshold for non-marketplace sales.

The Qualified Invoice System (適格請求書等保存方式), introduced on 1 October 2023, replaced the old simplified invoice system. Under the new system: (1) only businesses registered as 'qualified invoice issuers' can issue invoices that allow buyers to claim input tax credits; (2) qualified invoices must include: your JCT registration number (T+13 digits), tax rate, tax amount, and total price; (3) buyers can only claim input tax credits if they receive and retain a qualified invoice. This creates strong incentive for B2B sellers to register — if you don't register, business buyers will prefer registered competitors. The NTA publishes a public register of qualified invoice issuers at nta.go.jp.

The ¥10 million threshold is based on your taxable sales in the 'base period' — generally the fiscal year that ended two years before the current year. For example, for the fiscal year ending December 2026, the base period is the fiscal year ending December 2024. If your taxable sales (including those by your Japanese agents or permanent establishment) exceeded ¥10 million in that period, you must register for JCT from the beginning of the current year. New businesses: if your taxable sales in the first six months of the current year exceed ¥10 million AND your estimated sales for the full year exceed ¥10 million, you must register from the following year. Once registered, you must file JCT returns annually.

Non-Japanese sellers without a Japanese business address can register through a Japanese tax agent (税理士, zeirishi). The process: (1) appoint a tax agent, (2) submit Form 11 (application for JCT registration) to your jurisdictional Tax Office via the agent, (3) provide: company registration documents, proof of Japanese sales (e.g., Amazon seller account, website), estimated Japanese turnover, and bank details for JCT refunds. The tax agent will also handle JCT return filing and correspondence with the NTA. Registration typically takes 1-4 weeks. You will receive a JCT registration number (T + 13 digits) which must be displayed on qualified invoices.

JCT returns are filed annually. The filing deadline is within 2 months of the end of the fiscal year (e.g., if your fiscal year ends 31 March, the deadline is 31 May). Payment is due at the same time. For businesses with JCT liability exceeding ¥480,000 in the previous year, interim returns and payments are required (twice or four times per year depending on the amount). Late filing penalty: 15-20% of the tax due. Late payment penalty: 14.6% per annum (reduced to 7.3% for the first month). Underpayment penalty: 15-20% if the assessed tax exceeds the declared tax by more than the higher of ¥500,000 or 10% of the declared tax. Non-Japanese sellers file through their tax agent.