The EU says a UK move to unilaterally extend grace periods for Irish Sea border checks will be a breach of international law.
NI 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.
Mr Šefčovič is due to meet the UK’s Brexit Minister Lord Frost on Wednesday evening.
He added that the EU will respond in accordance with the “legal means” established by the protocol and the wider Brexit deal.
Irish Foreign Affairs Minister Simon Coveney said the UK government’s move “clearly undermines” 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 NI Secretary Brandon Lewis when speaking to them earlier on Wednesday.
The grace period affects supermarkets and other retailers, which face having to provide export health certificates for all shipments of animal products.
In a statement, the government said: “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.
“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.
The Northern Ireland Protocol is part of the Brexit deal which prevents a hardening of the land border between Northern Ireland and the Republic of Ireland.
It does that by keeping Northern Ireland in the EU single market for goods.
That has created a new trade border with Northern Ireland and the rest of the UK.
Unionists oppose the protocol, arguing that it has damaged internal trade from GB to NI and poses a risk to the future of the UK union.
But anti-Brexit parties in NI say that it must be implemented in full, and that issues should be worked out through joint UK-EU processes.
NI’s Deputy First Minister Michelle O’Neill has criticised the move.
“The EU and the British government need to work together and this appears to be another unilateral attempt to override what has been agreed,” she said.
“What everyone should be focused on is achieving agreement to find solutions to the issues that are outstanding, but it’s very clear the protocol must be made to work.”
Earlier on Wednesday, Theresa May’s former Brexit adviser, Raoul Ruparel, tweeted that it is “hard to see how this is allowed under the protocol”.
“I suspect UK gamble is that because its temporary & part of step to full requirements the scope for EU objection/action is limited,” he said.
Aodhán Connolly, of the Northern Ireland Retail Consortium, said it would allow “us to continue to give Northern Ireland households the choice and affordability they need”.
Extending the grace periods delivered “short-term stability”, he added.
“We now need the EU and the UK to show that they have the political will to live up to their side of the bargain by delivering a pragmatic, workable, risk-based solution.”
The government said further guidance will be provided later this week on a grace period for parcel movements from GB to NI.
It is due to to end on 1 April, meaning all parcels would need customs declarations.
Guidance will also be set out in regard to the issue of soil attached to the movement of plants, seeds, bulbs, vegetables and agricultural machinery.
Under the terms of the NI Brexit deal, soil from Great Britain is not permitted to enter Northern Ireland as it conflicts with EU plant regulations.