Japan Tax & Legal Consulting

Corporate Tax, JCT, Qualified Invoice System, and Transfer Pricing — Simplified

Japan Tax & Legal Consulting

Japan Tax & Legal Consulting

Corporate Tax, JCT, Qualified Invoice System, and Transfer Pricing — Simplified

Last Updated: March 2026 · Reading Time: ~10 min


Japan's Tax Stack at a Glance

Japan taxes businesses at national + local levels simultaneously. The effective combined rate varies by size and location, but most companies see 30–34%.

┌─────────────────────────────────────────────────────────┐
│                   JAPAN CORPORATE TAX STACK              │
├─────────────────────────────────────────────────────────┤
│  National Corporate Tax          │  23.2%  (standard)   │
│  Local Corporate Tax             │  10.3% of nat'l tax  │
│  Enterprise Tax (事業税)          │  3.5%–7% (progressive)│
│  Special Local Corporate Tax     │  % of enterprise tax  │
│  Inhabitant Tax (住民税)          │  ~12.9%–16.3% + levy │
├─────────────────────────────────────────────────────────┤
│  💡 Effective Combined Rate      │  ~30%–34% (Tokyo)    │
└─────────────────────────────────────────────────────────┘

📌 Official Source: NTA — Corporation Income Tax


1. Corporate Income Tax — Key Numbers

Standard Rates (FY starting Apr 2024+)

Category Rate Applies To
Standard 23.2% Taxable income (capital > ¥100M)
SME reduced 15% First ¥8M of income (capital ≤ ¥100M)
Surtax 10% of tax May apply to large corporations

Filing Requirements

Item Rule
Fiscal year Company's choice (any 12-month period)
Filing deadline 2 months after fiscal year-end
Extension +1 month if Articles require shareholder approval of financials
Interim payment Required if prior year tax > ¥200,000

2. Japan Consumption Tax (JCT)

How JCT Works

 Supplier                    Your Company                  Customer
    │                            │                            │
    │  sells goods + 10% JCT    │  sells goods + 10% JCT    │
    │──────────────────────────→│──────────────────────────→│
    │                            │                            │
    │  INPUT TAX (paid)          │  OUTPUT TAX (collected)    │
    │                            │                            │
    │                     ┌──────┴──────┐                     │
    │                     │  JCT RETURN │                     │
    │                     │             │                     │
    │                     │  Output ¥X  │                     │
    │                     │ − Input ¥Y  │                     │
    │                     │ = Pay ¥(X−Y)│                     │
    │                     └─────────────┘                     │

Key JCT Numbers

Item Detail
Standard rate 10%
Reduced rate 8% (food/beverages excl. alcohol & dining out; newspapers)
Taxable threshold ¥10M in taxable sales (base period = 2 years prior)
Below threshold Tax-exempt (免税事業者) — but can elect to be taxable
Filing frequency Annual (quarterly/monthly if elected or required)

📌 Official Source: NTA — Consumption Tax


3. Qualified Invoice System (QIS) — Since Oct 2023

Why QIS Matters

Before QIS: Any invoice supported input tax credit deduction. After QIS: Only invoices from registered Qualified Invoice Issuers support deductions.

What Must Be on a Qualified Invoice

# Required Element
1 Issuer name + Registration number (T + 13-digit corporate number)
2 Transaction date
3 Description of goods/services
4 Total amount, broken down by tax rate (8% / 10%)
5 Consumption tax amount per rate category
6 Recipient name

Transitional Measures — Credit for Purchases from Non-Registered Businesses

Period Credit Allowed
Oct 2023 → Sep 2026 80% of JCT
Oct 2026 → Sep 2029 50% of JCT
After Sep 2029 0%

Impact by Company Type

Type What to Do
🏢 Large corporation Register as QI Issuer; integrate Peppol e-invoicing
🏪 SME (taxable) Register; use QIS-ready accounting software (freee, Money Forward, Yayoi)
🏠 Tax-exempt small business Decide: register (become taxable) or risk losing B2B customers
🌏 Foreign company (no JP entity) Register via paper application to NTA; appoint JCT Tax Representative

📌 Official Source: NTA — Invoice System Outline (EN PDF)


4. Withholding Tax

Domestic Law Rates

Payment Type Resident Non-Resident
Dividends 20.42% 20.42%
Interest 20.42% 20.42%
Royalties Income tax 20.42%
Service fees (JP source) Varies 20.42%

Treaty Benefits

🌐 Japan has 80+ tax treaties that can reduce or eliminate withholding tax. Always check the applicable treaty before structuring cross-border payments.

Example Treaty Dividends Interest Royalties
🇺🇸 USA 10% / 0% 10% / 0% 0%
🇬🇧 UK 10% / 0% 10% / 0% 0%
🇭🇰 Hong Kong 5% / 10% 10% / 0% 5%
🇸🇬 Singapore 5% / 15% 10% 5%
🇰🇷 Korea 5% / 15% 10% 10%

Rates are illustrative and subject to treaty conditions. Verify with the actual treaty text.

⚠️ The payer in Japan bears responsibility for withholding. Failure to withhold = liability on the payer, not the payee.


5. Transfer Pricing

The Arm's Length Principle

 Japan subsidiary  ←──── transaction ────→  Foreign parent/affiliate
                          │
                          ▼
              Must be priced at arm's length
              (独立企業間価格)
              
 "Related party" = 50%+ voting rights or substantive control

Accepted Methods

Method Abbreviation Best For
Comparable Uncontrolled Price CUP Commodity transactions
Resale Price RP Distribution companies
Cost Plus CP Manufacturing / service providers
Transactional Net Margin Method TNMM Most common in practice
Profit Split PS Highly integrated operations
Discounted Cash Flow DCF Hard-to-value intangibles (since 2019)

Documentation Requirements (BEPS Action 13)

Document Required When Deadline
🌐 Master File Group consolidated revenue ≥ ¥100B With annual return
📋 Local File Related-party transactions ≥ ¥5B (or ¥300M for intangibles) With annual return
🗺️ CbCR Group consolidated revenue ≥ ¥100B 12 months after FY-end

💡 Pro Tip: Even below mandatory thresholds, maintain contemporaneous documentation. The NTA can request it during audits, and absence shifts the burden of proof.

Advance Pricing Agreements (APA)

Feature Detail
Type Unilateral or bilateral
Duration Typically 3–5 years (with possible rollback)
Japan's program One of the most active globally
Benefit Certainty on methodology; avoids double taxation

📌 Official Source: NTA — International Taxation


6. Digital Infrastructure

e-Tax (電子申告)

Feature Status
Corporate tax filing ✅ Supported
JCT filing ✅ Supported
Smartphone authentication ✅ Since Jan 2025 (Android)
Requirement for large corps Mandatory since 2020

Peppol e-Invoicing

Item Detail
Format PINT v1.1.1 (mandatory since May 2025 for connected entities)
Managed by Digital Agency (デジタル庁)
Compatible software Money Forward · freee · Yayoi
Benefit Machine-readable invoices; automated QIS compliance

7. Action Items for Foreign Companies

Priority Action
🔴 Immediate Register as Qualified Invoice Issuer if conducting B2B sales in Japan
🔴 Immediate Appoint JCT Tax Representative if non-resident
🟡 Within 3 months Review transfer pricing documentation for arm's length compliance
🟡 Within 3 months Confirm withholding tax treaty positions on all cross-border payments
🟢 Ongoing Maintain contemporaneous TP documentation
🟢 Ongoing File corporate tax + JCT returns on time

Official References

Source Link
NTA — English Portal nta.go.jp/english
NTA Report 2025 nta.go.jp/.../2025e.pdf
NTA — Invoice System nta.go.jp/.../consumption_tax
Special Taxation Measures Act (EN) japaneselawtranslation.go.jp
Corporation Tax Act (EN) japaneselawtranslation.go.jp
EU-Japan Centre — QIS eu-japan.eu

This article is for informational purposes only and does not constitute tax or legal advice. Consult a licensed tax accountant (税理士) or certified public accountant (公認会計士) for your specific situation.

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