The European Commission has said the decision by DUP Agriculture Minister Edwin Poots to halt agri-food checks at Northern Ireland ports creates “further uncertainty and unpredictability”.
It comes as the status of Brexit checks at ports remained unclear on Thursday morning after a deadline passed for a ministerial order to halt them.
Mr Poots issued the unilateral direction on Wednesday evening, instructing officials to stop the agri-food checks at midnight.
However, there has been no confirmation from Stormont officials whether they intend to comply with the order.
DUP rivals at Stormont insist Mr Poots’ direction is unlawful and civil servants are obliged to follow the law at all times.
An EC spokesperson said: “The European Commission has been working tirelessly with the UK Government to address practical challenges related to the implementation of the protocol.
“The decision by the Northern Irish Minister for Agriculture (Edwin Poots) is therefore unhelpful.
“It creates further uncertainty and unpredictability for businesses and citizens in Northern Ireland.
“The European Commission will closely monitor developments in Northern Ireland pursuant to this announcement.”
The spokesperson added: “Vice president Maros Sefcovic will speak to the UK Foreign Minister Liz Truss on Thursday afternoon to continue our discussions on finding durable solutions for the people of Northern Ireland.
“He will recall that controls on goods arriving in Northern Ireland from Great Britain are a key element of the protocol.
“They are necessary for Northern Irish business and citizens to continue to benefit from access to the single market for goods.
“They are also necessary to avoid a hard border on the island of Ireland.”
Lorries were still being received at a Department of Agriculture, Environment and Rural Affairs (Daera) checking facility in Belfast Port earlier on Thursday morning.
Several vehicles entered the facility after the ferry arrived from Cairnryan in Scotland at 6am.
A staff member declined to confirm to the PA news agency whether the agri-food checks required under the Northern Ireland Protocol were continuing.
The picture is further clouded due to the fact some of the port checks have been delegated to local council staff while UK Border Force personnel also have a presence at the facilities. It is unclear what would happen to their roles if the Daera staff withdrew.
Mr Poots’ direction only relates to the sanitary and phytosanitary (SPS) checks required by the protocol. The customs procedures on Irish Sea trade are unaffected by his instruction.
Announcing the move on Wednesday, Mr Poots said legal advice he had sought on the issue supported his view that he was entitled to stop the checks.
The UK Government has said it will not intervene in what it has characterised as a matter that falls within the Stormont Executive.
Government critics dispute this contention, highlighting that the UK has a duty under international law to abide by the terms of the Brexit Withdrawal Agreement.
Northern Ireland Secretary Brandon Lewis has denied claims the development is a “stitch-up” between the Government and the DUP.
“No, absolutely not,” he told ITV on Wednesday night. “This is a decision that the minister in Northern Ireland has taken.”
Mr Poots’ order came after he last week failed to secure the wider approval of the Stormont Executive to continue checks on agri-food produce arriving in Northern Ireland from Great Britain.
The minister argues that in the absence of Executive approval he no longer has legal cover to continue the documentary checks and physical inspections.
His bid to seek a ministerial vote at the Executive last week was branded an electoral stunt by other parties.
They insist the Executive has already agreed that Mr Poots’ department has responsibility for carrying out the checks and he does not have the authority to halt processes that are required under the Withdrawal Agreement, an international treaty.
The dispute centres on whether Mr Poots needs the authority of the wider Stormont Executive to conduct the checks.
Claiming recent court rulings have clarified that such authority is required, Mr Poots tried to secure the approval of the Executive by asking for the matter to be considered at last Thursday’s meeting.
He did so in the knowledge that if the issue was elevated to the Executive, his party could at that point exercise a veto to block approval for the checks.
Realising that, Sinn Fein used its own veto to prevent the issue from getting on the agenda.
The episode is playing out as the UK and EU continue negotiations aimed at reducing the number of checks required by the protocol.
