South African indirect tax amendments: Customs & Excise, VAT and Carbon Tax

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2026 Draft Taxation Amendment Bill includes several indirect tax proposals with practical implications for importers, exporters, special economic zoneparticipants and businesses exposed to carbon tax. Although the proposals are still subject to the legislative process, affected businesses should assess their likely impact on pricing, contracts, systems, compliance processes and financial forecasts.

Continuation of Customs, Excise, and VAT schedule amendments

2026 Draft Taxation Amendment Bill provides for the continued validity of specific amendments to the schedules of the Customs and Excise Act, 1964 and the VAT Act, 1991, including tariff, customs duty, excise duty, environmental levy, fuel levy, diesel refund and VAT-related schedule amendments that were implemented through the annual Budget process or another prescribed effective date. The continuation provisions ensure that schedule amendments remain legally effective while completing the parliamentary approval process, thereby providing certainty for taxpayers and traders.

In addition, ongoing reforms to the diesel refund regime include the modernisation of the diesel refund administration system, the separation of diesel refund registration from VAT registration, the introduction of a dedicated Diesel Refund Registration platform and enhanced relationship management requirements between diesel users and suppliers. SARS has also implemented amendments affecting diesel refund calculations arising from fuel levy changes and continues to reform diesel refund administration and compliance processes.

Business impact: Importers, exporters, manufacturers, warehouse operators, fuel users and finance teams should review the specific Customs, Excise and VAT schedules affected by recent amendments and ensure that tariff classifications, customs duties, excise duties, fuel levies, diesel refund entitlements, rebates, VAT treatments, import processes and export procedures remain aligned with the effective legislation and schedules. Particular attention should be paid to changes implemented from Budget Day or another specified effective date, as incorrect application may result in customs declaration errors, underpayments or overpayments of duty and VAT, diesel refund exposures, non-compliance with customs procedures, inaccurate landed costs, pricing impacts and potential difficulties recovering amounts from customers. Organisations that claim diesel refunds should also assess whether their registration, record-keeping, logbooks, supplier relationships and internal controls are aligned with SARS’ revised diesel refund framework and modernisation initiatives.

VAT zero-rating for services supplied to special economic zone operators

A proposed amendment to section 11(2)(k) of the VAT Act revises the wording governing the zero-rating of qualifying services physically rendered to a special economic zone (SEZ) operator. The amendment appears intended to clarify the circumstances in which the zero rate applies.

Why this matters: The wording could affect whether services supplied to SEZ operators qualify for zero-rating and whether the benefit remains limited to services physically performed within a customs-controlled area. Vendors should not assume that every service supplied to an SEZ operator qualifies for the zero rate.

Recommended action: Review service agreements, the location where services are physically performed, the status of the recipient and the documentary evidence supporting zero-rating. Where the treatment is uncertain, businesses should consider obtaining advice before issuing invoices or claiming adjustments.

Carbon budget tax refunds

The proposed amendment to section 17A of the Carbon Tax Act clarifies when taxpayers may claim refunds for compliance with an approved carbon budget. Under the proposal, refunds relating to the first two tax periods may be claimed in the third year, while refunds relating to years three to five may be claimed in the sixth year

Business impact: The proposal gives taxpayers a clearer timetable for refund claims, but it may delay the cash-flow benefit. Companies should align carbonbudget monitoring, verification records and refund forecasts with the revised claim periods.

Recommended action: Model the timing and value of expected refunds, confirm that emissions data can be reconciled to carbon tax returns, and retain evidence demonstrating performance against the approved carbon budget.

Proposed emissions-based threshold for commercial and institutional activities

The proposed amendment replaces the existing 10 MW(th) threshold with an emissions-based threshold of 25,000 tonnes of carbon dioxide equivalent. This would link the threshold more directly to actual greenhouse-gas emissions rather than installed thermal capacity.

Business impact: Some commercial and institutional facilities that were previously outside the carbon tax net may become subject to registration, measurement, reporting and payment obligations. Groups with multiple facilities should also consider whether emissions are monitored consistently across the organisation.

Key actions for affected businesses

Confirm which draft amendments apply to the group’s imports, exports, SEZ activities and emissions profile.

Review tax codes, tariff classifications, invoicing rules and system configurations.

Reassess contracts and pricing where indirect tax costs may change.

Strengthen supporting documentation for VAT zero-rating and carbon tax refunds.

Model cash-flow, provisioning and effective tax-cost impacts.

Brief finance, legal, procurement, logistics, sustainability and operational teams before the rules take effect.

SNG Grant Thornton perspective: The proposals reinforce the need for indirect tax and environmental tax compliance to be managed as operational risks, not only as tax-return obligations. Businesses should use the legislative lead time to validate system settings, clarify uncertain VAT treatments, improve emissions data governance and quantify the financial impact before the amendments are enacted.

Botswana Customs Amendment Act, 2026: executive summary for CFOs and in-house legal teams

Botswana’s Customs Amendment Act, 2026 materially increases customs compliance, enforcement and debt-recovery risk for businesses involved in cross-border trade. CFOs should assess the impact on landed cost, working capital, customs debt, penalties and provisioning. In-house legal teams should review contracts, delegation frameworks, customs records and escalation procedures to ensure the business can respond quickly to BURS audits, third-party recovery notices, seizures and disputes.

Botswana Customs Amendment Act, 2026: concise client alert

Botswana’s Customs Amendment Act, 2026 introduces significant changes to the country’s customs framework. The amendments modernise customs administration, expand BURS enforcement powers, strengthen debt-recovery mechanisms and introduce clearer rules for valuation, origin, Special Economic Zones and customs assessments.

The Act is relevant to importers, exporters, logistics providers, SEZ participants, businesses using preferential trade arrangements and companies that may hold money for, or trade with, customs debtors. The reforms are effective from 1 July 2026, giving affected
organisations limited time to strengthen customs governance and readiness.

What has changed?

The key changes affect importer and exporter responsibilities, advance binding rulings, BURS enforcement powers, departure and aircraft reporting, customs valuation, customs debt, third-party recovery, seizure powers, intellectual property border protection, SEZs, rules of origin and the period within which customs assessments may be raised.

Key implications for business

Broader customs responsibility: The expanded definitions of “importer”, “exporter” and “goods” may extend responsibility to persons acting on behalf of, representing or having a beneficial interest in goods. Businesses should confirm who bears customs responsibility under logistics, agency, financing and sale agreements. Greater certainty, but higher scrutiny: Advance binding rulings may help reduce disputes on classification, valuation and origin. At the same time, customs valuation rules are being updated, which may increase scrutiny of related-party pricing, royalties, licence fees, transport costs and supporting documentation.

Confirm customs responsibility across import, export, agency and freight-forwarding arrangements.
Review valuation support for related-party imports, royalties, licence fees and transport or insurance charges.
Consider advance binding rulings where classification, valuation or origin positions are uncertain.

Customs debt, enforcement and third-party exposure

The Act gives customs debt clearer legal status and allows BURS to pursue recovery through partial-payment arrangements, continued enforcement and third-party recovery notices. BURS may recover unpaid customs debts from persons who hold money for, bank, employ or owe money to a customs debtor. procurement bodies and regulators regarding gender balance in leadership structures.

Business impact: CFOs should treat customs debt as a live financial risk and review cash-flow forecasts, provisioning, settlement authority and exposure to third-party recovery notices. Legal teams should ensure there is a clear process for validating and responding to BURS notices.

Operational border risks

BURS and customs officers have broader powers to detain goods, seize goods and transport, retain electronic records and devices, and forfeit property used in customs violations. The Act also introduces additional departure-reporting obligations and advance reporting requirements for aircraft operators.

Business impact: Border delays, detention or seizure can quickly affect supply chains, customer commitments and cash flow. Companies should brief customs brokers, logistics providers, border staff and internal legal, tax and finance teams on escalation steps.

SEZs, origin and intellectual property

The Act introduces dedicated rules for SEZs, more detailed origin provisions and border protection measures for intellectual property rights. These changes affect companies operating in SEZs, claiming preferential duty treatment, importing branded goods or managing regional supply chains.

Business impact: SEZ procedures, inventory controls, duty treatments, supplier declarations, certificates of origin and licence documentation should be reviewed before the effective date. Incorrect origin claims or inadequate product-authenticity records may result in duty exposure, delays or disputes.

Assessment period and document retention

The amendments introduce a five-year limitation period for customs assessments and reassessments, with exceptions for fraud, misrepresentation, material non-disclosure, certain court-ordered reassessments and settlement agreements.

Business impact: The limitation period provides greater certainty, but businesses still need robust records. Customs documentation, valuation evidence, origin support, contracts and BURS correspondence should be retained for at least the assessment period and longer where audits or disputes are ongoing.

Key actions for CFOs and in-house legal teams

Affected businesses should use the period before implementation to confirm customs responsibilities, test valuation and origin support, review contractual protections and strengthen procedures for managing BURS audits, seizures, settlement discussions and recovery notices.

Map customs responsibilities across importers, exporters, agents, freight forwarders, SEZ operators and group companies.
Update procedures for responding to BURS audits, seizure notices, garnishee notices and information requests.
Strengthen rules-of-origin documentation for goods traded under preferential trade arrangements.
Review customs valuation positions, especially related-party transactions, royalties, licence fees and transport or insurance charges.
Review SEZ operating procedures, inventory controls, customs declarations and duty treatment.
Ensure customs records are retained for the limitation period and are readily available during audits or disputes.
Confirm controls over customs debt, provisioning, partial-payment arrangements and settlement authority.

SNG Grant Thornton perspective: The Botswana Customs Amendment Act, 2026 should be treated as a governance and risk-management issue, not only as a customs technical update. CFOs should assess the potential impact on landed cost, cash flow, penalties, customs debt and provisioning. In-house legal teams should review contracts, delegation frameworks, documentation standards and escalation processes. Businesses that prepare early will be better placed to manage BURS queries, defend customs positions and avoid operational disruption at the border.

Article by: Sipho Mhaga (Africa Desk- Cross Border Trade Expert)

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Tax bulletin: Global, indirect tax and mobility updates

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Khanyisa Cingo-Ngandu

Raeesa Haneef

Mbusi Mthwane - GTP(SA)

Sipho Mhaga

Nokukhanya Madilonga - CA(SA)

Ellaine Raboroko TA(SA)

Tax bulletin: Global, indirect tax and mobility updates

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Tax bulletin: Global, indirect tax and mobility updates

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Tax bulletin: Global, indirect tax and mobility updates