A major dispute has erupted between the Organised Private Sector of Nigeria (OPSN) and the Nigeria Revenue Service (NRS) over the implementation of the country’s new tax laws, Daily Trust can report.

The controversy follows a directive issued by the NRS requiring companies yet to file their Companies Income Tax (CIT) returns for the 2026 Year of Assessment to do so under the provisions of the Nigeria Tax Act (NTA) 2025 and the Nigeria Tax Administration Act (NTAA) 2025, both of which came into effect on January 1, 2026.

However, the OPSN, which represents more than 40 employers’ associations, chambers of commerce and business organisations across the country, has accused the revenue agency of acting contrary to the Federal Government’s official transition guidelines and has called for urgent presidential intervention to avert what it described as a growing tax administration crisis.

The NRS is yet to respond to the concerns raised by the OPS.

Daily Trust reports that the federal government had last week issued implementation guidelines on the implementation of the Tax Acts 2025, as part of the transition process from repealed tax laws to Nigeria’s new tax framework.

According to the document, the Tax Acts 2025 — comprising the Nigeria Revenue Service (Establishment) Act, the Nigeria Tax Act, the Nigeria Tax Administration Act, and the Joint Revenue Board (Establishment) Act — will apply from their respective commencement dates as stipulated in the laws.

The ministry said tax liabilities, assessments, audits, investigations, disputes and enforcement actions relating to periods before January 1, 2026, will be treated under the repealed tax laws.

“Tax returns relating to accounting periods ending before January 1, 2026, will be filed under the previous tax laws, while returns falling due from January 1, 2026, onward will be administered under the new tax framework,” the statement reads.

The guidelines issued by the federal ministry of finance partly read: “The Acts shall apply prospectively from the date of commencement, except where expressly provided to the contrary in the Acts as a specific matter rather than a general rule.

“No tax, penalty, surcharge, interest, filing obligation, or administrative requirement under the Acts shall apply to any period prior to its commencement. Where an assessment, compliance, or enforcement action relates to a period before commencement, such assessment, compliance or enforcement action shall be governed by the law applicable to that period.”

The guidelines also explicitly kick against retroactive application, stating under Part 3 that ‘No taxpayer shall be assessed based on provisions of the Acts with respect to taxes on a transaction, supply, or disposal occurring before the commencement date.”

However, a memo to taxpayers by the NRS dated 23rd June, 2026, a few days after the guidelines approved by the Minister of Finance and Coordinating Minister for the Economy, Mr. Taiwo Oyedele, directed taxpayers especially companies to file their Companies Income Tax return due in 2026 under the NTA and NTAA, ‘except where there is an express statutory saving or transitional provision that specifically applies to the relevant matter.”

Some of the companies who spoke with our correspondent yesterday insisted that the new memo issued by the NRS was not in tandem with the Ministerial guidelines which clearly prevent retroactive application of the new tax laws.

The memo, they said, asked the companies to file returns for the 2025 accounting period using the new laws.

“For God’s sake, one expects alignment by the MDAs on the Ministerial directive,” one taxpayer, a chartered accountant said.

However, in an open letter addressed to President Bola Ahmed Tinubu and jointly signed by the leadership of key private sector bodies, including the Manufacturers Association of Nigeria (MAN), the Nigerian Association of Small and Medium Enterprises (NASME), the Nigerian Association of Small Scale Industrialists (NASSI), the Nigerian Association of Chambers of Commerce, Industry, Mines and Agriculture (NACCIMA), and the Nigeria Employers’ Consultative Association (NECA), the group warned that the conflicting interpretations of the new tax laws have effectively paralysed corporate tax filings across the country.

The OPSN said it fully supports the administration’s tax reform agenda and remains committed to lawful tax compliance, but argued that the implementation approach adopted by the NRS undermines the spirit and intent of the reforms.

“This Open Letter is not an attack on tax reform or lawful revenue mobilisation,” the group stated.

“It is a plea to preserve the legality, credibility and economic promise of the historic reforms championed by Your Excellency. Our members are willing and ready taxpayers. They seek a clear, lawful and functional framework through which they can file accurate returns, pay taxes already accrued to the Federation, protect jobs and continue investing in Nigeria.”

The dispute centres on how taxes relating to accounting periods that ended before January 1, 2026 should be treated.

According to the OPSN, the General Transition Guidelines issued by the Minister of Finance and Coordinating Minister of the Economy pursuant to provisions of the NTAA 2025 and NTA 2025 clearly state that tax obligations arising from accounting periods ending before the commencement date of the new laws should continue to be governed by the repealed tax laws, even if the filing and payment deadlines fall in 2026.

The private sector groups noted that the guidelines expressly provide that the new tax laws apply prospectively from January 1, 2026, except where specific provisions state otherwise.

The guidelines further state that no tax, penalty, surcharge, interest, filing obligation or administrative requirement under the new Acts should apply to any period before commencement.

They also stipulate that Companies Income Tax payable for any basis period ending before January 1, 2026 should be determined under the repealed Companies Income Tax Act, notwithstanding that filing and payment may become due after the commencement date.

However, the OPSN alleged that the NRS has adopted a different interpretation.

The controversy intensified after the NRS Emerging Taxpayers Office in Abuja issued a notice dated June 23, 2026 directing companies yet to file their Companies Income Tax returns for the 2026 Year of Assessment to do so under the new NTA and NTAA framework.

The notice stated that the NRS had no statutory authority to process Companies Income Tax returns for the 2026 Year of Assessment under the repealed Companies Income Tax Act or any other repealed tax legislation.

“The applicable law for filing is determined by statute and not by taxpayer election, publication, administrative discretion, advisory, or any other communication suggesting an alternative filing basis,” the notice said.

“The Service has no statutory authority to process Companies Income Tax returns for the 2026 Year of Assessment under the repealed Companies Income Tax Act or any other repealed tax legislation.”

But the OPSN which hitherto commended the federal government for the issuance of the guideline, described the position as a direct contradiction of the Federal Government’s transition guidelines and warned that businesses are now caught between conflicting directives.

“The Federal Government’s Guidelines state that the repealed laws govern such periods notwithstanding a later filing date, while the NRS communication asserts that the new Acts govern because the return is due in 2026,” the group stated.

“The issue is not whether the NTA and NTAA commenced on 1 January 2026; the issue is which substantive rules govern profits, transactions and obligations that arose in a basis period already concluded before commencement,” the OPSN added.

According to the OPSN, allowing the contradiction to persist would place taxpayers in an impossible position.

“To permit this contradiction to persist would weaken the coherence of Executive governance and place taxpayers in the impossible position of choosing between an official Federal Government directive and an inconsistent revenue-administration instruction,” the group warned.

The organised private sector also raised concerns about the legal implications of the NRS position, arguing that it potentially violates established principles of fiscal and administrative law.

Among the concerns highlighted are the principles of non-retroactivity, legal certainty, strict construction of taxing statutes, legitimate expectation and consistency in tax administration.

The OPSN argued that taxpayers who completed their 2025 financial activities under the legal framework existing at the time should not be compelled to recalculate tax liabilities under laws that came into effect after those activities had already been concluded.

The group maintained that tax burdens, rates, penalties and substantive obligations should not be imposed retroactively unless expressly authorised by legislation.

Beyond the legal issues, business groups warned that the dispute could have serious consequences for government revenue generation and economic stability.

According to the OPSN, many companies are currently unable to complete their tax filings because the tax administration platforms and filing systems have not been fully aligned with the transition framework.

The group noted that at a time when the government is seeking to improve revenue collection, any policy confusion that delays filings and payments is counterproductive.

“At a time when the Government requires every legitimate naira of revenue, a system that prevents willing taxpayers from filing and paying is fiscally counterproductive,” the letter stated.

The OPSN further argued that uncertainty surrounding the implementation of the new tax laws could discourage investment and weaken business confidence.

It warned that investors place a premium on predictability, transparency and consistency in tax administration, and that prolonged disputes over implementation could damage Nigeria’s reputation as an investment destination.

As the June 30 filing deadline approaches, stakeholders say urgent action is needed to prevent the disagreement from escalating into a broader tax administration and investment confidence crisis.