The EU says a UK move to unilaterally extend grace periods for Irish Sea border checks will be a breach of international law.
Northern Ireland has remained a part of the EU's single market for goods so products arriving from GB undergo EU import procedures.
The grace periods mean procedures and checks are not yet fully applied.
The first of these periods will expire at the end of March, but the UK has said it will be extended until October.
European Commission Vice President Maroš Šefčovič said the move amounted to "a violation of the relevant substantive provisions" of the Brexit deal on Northern Ireland, known as the NI Protocol.
He said the EU would respond in accordance with the "legal means" established by the protocol and the wider Brexit deal.
Following a call on Wednesday evening between Mr Šefčovič and Lord Frost, the Cabinet Office minister with responsibility for EU relations, a UK government spokesperson said "official-level notification" of the move was made to the commission earlier this week.
The spokesperson said Lord Frost underlined the extension was needed for "operational reasons" and such measures were "well precedented in other international trade arrangements, and that they were entirely consistent with our intention to discharge our obligations under the Protocol in good faith".
Irish Foreign Affairs Minister Simon Coveney said the UK government's move clearly undermined its commitment to the implementation of the protocol and described the unilateral decision as "deeply unhelpful".
He said he had made his regret over the decision clear to Lord Frost and Northern Ireland Secretary Brandon Lewis.
The grace period affects supermarkets and other retailers, which face having to provide export health certificates for all shipments of animal products.
"For supermarkets and their suppliers, as part of the operational plan the UK committed to at the UK-EU Joint Committee on 24 February, the current Scheme for Temporary Agri-food Movements to Northern Ireland will continue until 1 October," said a government statement.
"Certification requirements will then be introduced in phases alongside the roll out of the Digital Assistance Scheme."
It is understood the government is describing this to the EU as an "operational easement", rather than a formal extension of the grace period.
It is using the example of how the Irish government temporarily relaxed safety and security declarations on products arriving from GB in January.