Tax Confusion Festers as Finance Ministry, NRS Yet to Clarify 6 Key Points in 2025 Tax Acts.

By Godson Ikoro

With six months of the taxpayer enlightenment window already gone, strong indications have emerged that six confusing provisions in the Nigeria Tax Act 2025 and Nigeria Tax Administration Act 2025 remain unresolved.

The Federal Ministry of Finance and the Nigeria Revenue Service (NRS) are yet to clear ambiguities in the two laws that took effect on January 1, 2026. The confusion has persisted from January to June 2026, affecting taxpayers and government agencies.

Revolnews Online investigations this week reveal that the Ministry and NRS published Transition Guidelines in June 2026 — exactly six months after the laws became effective. Stakeholders say the guidelines are vague and lack the clarity needed for compliance.

“PDFs don’t reach Alaba Market or an MDA procurement desk,” a taxpayer told Revolnews Online. “The six-month enlightenment window ends when taxpayers understand, not when guidelines are uploaded.”

The 6 unresolved issues are:
● Basis Period vs. Filing Date Contradiction*
The June 2026 Transition Guidelines state that accounting periods ending before January 1, 2026 fall under the old law, while periods ending from January 1, 2026, fall under the new law. However, an NRS memo dated June 19 directed companies to file 2026 Year of Assessment returns under NTA/NTAA templates “regardless”.
Impact: Companies are unsure which rule applies. A plain-English notice clarifying “basis period vs. filing date” is needed to prevent penalties.
YOA means Year of Assessment — the tax year in which income is assessed by the revenue authority.

● Capital Gains Tax on 2025 Disposals.
A February 2026 NRS memo said gains from 2025 disposals remain under the old CGT Act at 10%. The new NTA now taxes gains on a “preceding year basis” at income tax rates. NRS is “expected to issue guidelines” on whether 10% CGT already paid for 2025 will be excluded from 2026 filings.
Impact: Taxpayers who paid 10% CGT in 2025 risk double taxation or filing errors without clear public guidance.

● Free Zone Entities’ 25% Domestic Sales Threshold*
From January 1, 2026, FTZ companies lose their blanket tax exemption. Tax applies if domestic sales exceed 25% of total sales. A three-year transition from 2026–2028 allows up to 25% exemption.
Impact: Most FTZ operators still believe they are “tax-free.” NRS needs to communicate the change across all channels to avoid audit shocks.

● E-Invoicing Real-Time Mandate.
E-invoicing is now law, and input VAT can only be claimed on invoices verified through the NRS portal. SMEs had requested an “easy onboarding window without retroactive penalties” before January 2026.
Impact: SMEs fear penalties. Civil society groups are demanding a step-by-step newspaper guide and a dedicated helpline.

● TIN Enforcement and ₦5 Million Contract Penalty.
Under NTAA 2025, agencies and companies awarding contracts to unregistered persons risk a ₦5 million penalty. Banks must also verify TINs.
Impact: Many SMEs and MDAs are unaware of the ₦5 million fine. A newspaper notice to procurement officers from NRS is overdue.

● 4% Development Levy and SME Exemptions.
A unified 4% Development Levy now replaces the IT Levy, TETFund, and others. Small businesses with turnover below ₦100 million are exempt from CIT, CGT, VAT, and the Development Levy.
Impact: Market confusion persists on VAT changes. NRS needs to publish a clear “what changed, and what didn’t” notice.

Stakeholders who spoke to Revolnews Online this week insist the six issues require immediate explanation via newspaper publications, online news platforms, and radio. This will ensure taxpayers and agencies are aligned.

“The January–June 2026 window was for enlightenment. The biggest gap now can be closed with simplified newspaper notices, online publications and radio,not more PDFs,” a stakeholder said.