Nigeria’s 2026 Tax Transition Guidelines: A Guide For Healthcare Businesses

1. Introduction

On 18 June 2026, the Federal Government,¹ through the Honourable Minister of Finance and Coordinating Minister of the Economy, issued² the General Transition Guidelines (“the Guidelines”) for the implementation of the 2025 Tax Reform Acts. These reforms comprise the Nigeria Tax Act 2025, the Nigeria Tax Administration Act 2025, the Nigeria Revenue Service (Establishment) Act 2025, and the Joint Revenue Board (Establishment) Act 2025 (collectively, “the Acts”).

The Guidelines aim to ensure consistent application during the implementation of the Acts and provide rules to assist taxpayers and other stakeholders transitioning from repealed tax laws to the new legislation. Furthermore, they seek to prevent retroactive application, resolve internal ambiguities or conflicts within the Acts, address external conflicts between the Acts and other laws, and provide operational clarity for tax authorities and taxpayers alike.

While this transitional framework applies across all sectors, it provides much-needed clarity for healthcare businesses. Hospitals, pharmaceutical manufacturers, digital health companies, medical laboratories, and Health Maintenance Organisations (HMOs) need to understand salient provisions within the Guidelines. Doing so will help them avoid regulatory pitfalls and meet compliance obligations as the new tax regime takes effect. Thus, this article examines the key provisions of the Guidelines that healthcare businesses must know.

2.0 Key Provisions

A. Commencement and Prospective Applications

The Guidelines apply to tax returns that fall due from 1^st January 2026. The commencement date is particularly significant because the Guidelines contain transitional provisions that clearly delineate the boundary between the old and new compliance regimes. In essence, the Guidelines are intended to operate prospectively rather than retrospectively. Accordingly, tax liabilities, penalties, surcharges, interest, filing obligations, and other administrative requirements introduced under the Acts, do not apply to periods preceding the Guidelines’ commencement.

Matters relating to tax periods before 1^st January 2026, including assessments, compliance reviews and enforcement actions, remain subject to the legal framework that was in force during those periods. For example, if a company has an accounting year ending 31^st December 2025, its Companies Income Tax return will ordinarily be due for filing in 2026 and will therefore be subject to the Guidelines. However, because the return relates to the 2025 year of assessment, any assessment, compliance review or enforcement action arising from that tax period will continue to be governed by the law applicable to the 2025 tax year. This approach provides certainty for taxpayers and ensures that obligations are assessed in accordance with the law applicable at the relevant time.

• Tax Disputes, Objections and Appeals

By virtue of the Guidelines, pending appeals or objections that were filed before the new Tax Acts were commenced (that is, before the 1^st of January 2026) shall continue under the rules of the old tax regime. This means that the new tax Acts shall not apply in the resolution of tax disputes, objections, and appeals in this category. This approach protects taxpayers from having ongoing disputes subjected retrospectively to a new procedural framework. However, according to the Guidelines, objections raised after 1^st January 2026 will be resolved in line with the procedure under the new Tax Acts, even where the objection relates to an assessment for an earlier year of assessment. A company is required to file its notice of objection within 30 days of receiving an assessment notice, while the tax authority is required to determine and communicate its decision on the objection within 90 days of receiving the notice of objection, failing which the objection is deemed to have been upheld.³

The Guidelines further provide that the transitional interpretation contained therein shall apply for dispute resolution purposes.⁴ This means that, in determining disputes arising during the transition, the relevant authority must apply the transitional interpretation set out in the Guidelines. Accordingly, while objections filed on or after 1^st January 2026 are to be processed under the procedural framework of the new Tax Acts, issues relating to the substantive tax liability, assessments, compliance, and enforcement actions for pre-commencement tax periods continue to be determined in accordance with the law applicable to those periods.

This is particularly relevant to healthcare businesses with ongoing audits, outstanding assessments, unresolved withholding tax or VAT exposures, and disputes relating to tax incentives or exemptions. Such businesses should maintain clear records of the relevant transaction dates, filing periods, assessments, objections, and correspondence with the relevant tax authority, as these will be important in determining the applicable legal and procedural regime.

• Income Tax Transition for Individuals and Companies

One of the most significant aspects of the Guidelines for healthcare businesses relates to the transitional rules governing income tax for both employees and corporate entities. For individuals in employment, the Guidelines provide that where Personal Income Tax (PAYE) for the 2025 tax year has been deducted and remitted monthly under the repealed tax laws up to December 2025, the filing of tax returns for the 2026 year of assessment shall continue to be governed by the repealed legislation. However, PAYE on employment income earned from 1^st January 2026 onwards will be administered under the new Tax Acts.

Similarly, individuals whose taxes are assessed through direct assessment will continue to be taxed under the repealed laws in respect of income earned during the 2025 tax year, notwithstanding that the returns are filed in 2026. Income earned from 1^st January 2026 will, however, be subject to the provisions of the new Tax Acts.⁵

For companies, the Guidelines distinguish between accounting periods ending before and after the commencement of the new regime. Company Income Tax (CIT) payable in respect of any basis period ending before 1^st January 2026 will continue to be assessed under the repealed legislation, even where the filing and payment obligations arise after the commencement of the new Acts. Conversely, income relating to any accounting period ending after the commencement date will be governed by the new Tax Acts. Take, for example, a company with an accounting year ending 31^st March 2026. Although part of its accounting period falls before 1^st January 2026, its basis period ends after the commencement date of the new Tax Acts. Accordingly, by virtue of the transitional provisions, the company’s income for that basis period will be assessed under the new Tax Acts, notwithstanding that a portion of the accounting period preceded their commencement. Conversely, where a company’s basis period ended on or before 31^st December 2025, the repealed tax legislation will continue to govern the assessment for that basis period.

Also, under the Guidelines, old levies, including the Tertiary Education Trust Fund (TETFund) Levy, NITDA Levy, and NASENI Levy applicable to accounting periods ending before 1^st January 2026, will continue to be governed by the repealed legislation and remain payable. However, accounting periods ending after the commencement date will instead be subject to the new 4% Development Levy established under the new Tax Acts, replacing the various earmarked levies under the former regime.

In addition, small and medium-sized companies will continue to be assessed under the tax rates and rules contained in the repealed legislation for basis periods ending before 1^st January 2026, while basis periods ending thereafter will be subject to the new tax framework. Notably, the Guidelines also permit a taxpayer, subject to the prior written approval of the relevant tax authority, to elect to file its income tax return for an accounting period ending before the commencement date under the provisions of the new Tax Acts where appropriate.⁶

For healthcare organisations, these transitional rules require careful review of payroll administration, corporate tax planning, accounting periods, and financial reporting systems to ensure that the correct legal framework is applied during the transition to the new tax regime.

• Transaction Taxes (Withholding Tax, Value Added Tax, and Stamp Duties)

The Guidelines also provide transitional rules for transaction-based taxes, including Withholding Tax (WHT), Value Added Tax (VAT), and Stamp Duties. They clarify that any goods delivered or services rendered on or before 31^st December 2025 will continue to be governed by the repealed tax legislation, regardless of when payment is ultimately received. Conversely, transactions occurring from 1^st January 2026 onwards will be subject to the new Tax Acts, except where payment was made in advance before the commencement date.

The Guidelines further address contracts that span both tax regimes. Where a contract was executed before the commencement date but continues to be performed after 1^st January 2026, only the portion of the contract performed after the commencement date will be governed by the new Tax Acts. Likewise, sums received before the commencement date will remain taxable under the repealed legislation, while payments received after commencement will be subject to the new tax regime.

• Resolving Legal and Regulatory Conflicts

The Guidelines not only acknowledge but anticipate that possible conflicts may arise from the provisions of the previous tax laws, interpretation of terms, regulations issued by tax authorities before the new Acts, exemption and filing requirements, and compliance provisions where more than one method of compliance is available. The Guidelines establish a hierarchy for addressing these conflicts, clarifying that where any conflict exists between the new and old Acts, the new Acts shall prevail. In the same vein, where two provisions within the new Acts appear to conflict, the preferred interpretation is the one that best reflects legislative intent, economic neutrality and administrative simplicity. Importantly, where there is a clear inconsistency between provisions of the Acts, the conflict is to be resolved in favour of the taxpayer.

Healthcare businesses should therefore check for inconsistencies by reviewing their internal tax policies and procedures against the new Acts and, where applicable, the repealed Acts, particularly in light of the transitional provisions. Where inconsistencies arise, clarifications should be sought from the relevant tax authority, which may issue further clarification by way of a public notice. 

Healthcare businesses should therefore monitor further guidance issued by the relevant tax authorities on the implementation of the new tax regime, especially in relation to regulated healthcare services, medical supplies, cross-border transactions, professional fees, and the application of existing tax incentives.

3.0 Compliance Checklist for Healthcare Businesses

In order to ensure a seamless transition to the new tax regime, healthcare businesses are advised to take the following steps:

1. Identify the relevant tax period. Determine whether a relevant transaction, supply, disposal, income or basis period falls before or after the 1^st of January 2026, as this will generally determine whether the repealed laws or the new Acts apply.

• Review income-tax treatment. Healthcare companies should confirm whether their accounting period ended before or after commencement, as this will determine the applicable income tax regime. Employers should also ensure that PAYE is correctly applied to compensation payable from January 2026.

• Review transaction taxes. Healthcare businesses should assess when goods were delivered and services rendered when determining the applicable WHT, VAT and stamp-duty treatment. This is particularly important for medical supplies, service contracts, consultancy arrangements, and long-term procurement agreements that span the transition date.
• Maintain adequate records. Businesses should retain records required under the repealed laws for the applicable statutory period, while updating their record-keeping systems to meet prospective obligations under the new Acts.

• Update filing and payment processes. Returns due before 1^st January 2026 should be filed under the existing procedures, while returns due on or after that date should follow the rules, forms and electronic templates issued under the new regime. Existing forms may remain valid pending the introduction of new ones.

• Review tax registrations and identification details. Healthcare businesses should ensure that their registration details are current and prepare for the standardisation or migration of taxpayer identification numbers into a unified system when implemented.

• Review outstanding disputes and assessments. Businesses with pending audits, objections, appeals or assessments should determine whether the matter is governed by the repealed laws or the new procedural framework. Objections filed after commencement will follow the procedures under the new Acts, even where the disputed assessment relates to an earlier period.

• Monitor further guidance. Businesses should monitor notices, regulations and clarifications issued by the relevant tax authority, particularly where there are unresolved conflicts, uncertainties in sector-specific treatment, or changes to filing, payment and documentation requirements.

4.0 Conclusion

The Guidelines provide clear directions to help taxpayers align with the new tax regime. As a general rule, the new Acts apply prospectively from the 1^st of January 2026. This means that taxes, penalties, rates, thresholds, filing obligations, and other requirements under the new framework should not be imposed on transactions that arose before that date. A safeguard is provided against retrospective application.

Pre-commencement matters remain governed by the repealed laws, while post-commencement matters fall under the new Acts, subject to the specific transitional rules in the Guidelines. Healthcare businesses should use this prospective approach to review their tax positions, contracts, records and outstanding disputes. Clear documentation of relevant dates and careful separation of transactions spanning both regimes will be essential to reducing exposure to incorrect assessments and ensuring a smoother transition into the new tax framework.

Given the technical nature of these transitional rules and the sector-specific nuances that may arise, healthcare businesses are encouraged to seek tailored legal and regulatory advice. Health Ethics and Law Consulting advises healthcare businesses navigating these transitional tax obligations and welcomes enquiries on regulatory compliance.

Footnotes

1. Samuel Anyanwu, ‘Federal Government Issues Transition Guidelines for Tax Acts 2025’ (Federal Ministry of Information and National Orientation, 18 June 2026) https://fmino.gov.ng/federal-government-issues-transition-guidelines-for-tax-acts-2025/ accessed 5 July 2026.

2. The Minister issued these Guidelines pursuant to powers conferred under Section 144 of the Nigeria Tax Administration Act 2025 and Section 200 of the Nigeria Tax Act 2025.

3. Section 41 of the Nigeria Tax Administration Act.

4. Clause 7(3) of the Guidelines.

5. Clause 10.1 of the Guidelines.

6. Clause 10.1.2 of the Guidelines.

The content of this article is intended to provide a general guide to the subject matter. Specialist advice should be sought about your specific circumstances.