The EU's Chief Brexit negotiator has described the decision by the DUP Agriculture Minister to suspend Protocol agri-food checks as "very unhelpful".
Yesterday, Stormont's Agriculture Minister Edwin Poots instructed officials in his department to stop all checks on goods coming into Northern Ireland from midnight after receiving legal advice.
Following his video conference with the UK's Chief Negotiator, Foreign Secretary Liz Truss, Maroš Šefčovič said that it creates "uncertainly and unpredictability" for the people and businesses in Northern Ireland.
"These checks are necessary for Northern Ireland to benefit from access to the EU's Single Market for goods," Mr Šefčovič said.
"According to our information, officials in Northern Ireland continue to carry out checks on goods coming to Northern Ireland. It is essential that this remains the case. The European Commission will closely monitor the developments on the ground."
He added that the protocol was the "cornerstone of the Withdrawal Agreement" and is an international agreement.
"It is therefore the UK government's responsibility to uphold its legal obligations stemming from the protocol – the only solution we have found with the UK government to protect the Good Friday Agreement, taking into account the type of Brexit the UK government chose.
"It is by respecting our international obligations and living up to our responsibilities, that trust is built and maintained, also in the future."
This evening, a spokeswoman for Northern Ireland's Department of Agriculture, Environment and Rural Affairs said: "DAERA officials have not refused the Minister’s instruction, however, they are currently considering the wider implications of fulfilling the Minister’s request."
Earlier, the British government said it was not aware of the DUP decision, Prime Minister Boris Johnson's official spokesman has said.
"As we speak checks are continuing to take place at ports in Northern Ireland, as they have done before," Mr Johnson's spokesman said.
"We are monitoring the situation closely and keeping the legal position under review."
Asked if Mr Johnson would like to see the checks continue, the spokesman said: "Yes, we would like this situation to be resolved, recognising it is a matter for the Northern Ireland Executive."
Pressed on whether the checks could be carried out at ports in Great Britain rather than on arrival in Northern Ireland, the spokesman said: "We are looking into the legal position."
The spokesman added: "We certainly weren't aware that this was the approach the DUP were going to take.
"I'm not sure what preparatory work has gone on, on the basis this could happen."
The government's focus was on resolving the issues around the protocol, the spokesman said.
Because there had been no warning in advance, there were no contingency plans put in place to carry out customs and SPS checks at ports in Britain, such as Liverpool and Cairnryan.
The spokesman denied that the DUP's action suited the Prime Minister's aims, as it highlighted problems with the operation of the protocol.
He said: "No, I wouldn't agree with that".
He said the problems of the protocol are already very clear, and the British government wants them resolved in talks with the EU.
EU satisfied checks are continuing
European Commission spokesman Eric Mamer said the EU's observers in Northern Ireland were satisfied the required checks were still being carried out.
"We have seen this announcement, obviously we are monitoring the situation on the ground - we have experts who are on the ground in Northern Ireland precisely in relation to the issue of checks," he said.
The "preliminary information" from those experts "is indeed that those checks are continuing".
Asked if the entire Brexit trade deal with the UK could be suspended if the Northern Ireland Protocol's requirements were not met, Mr Mamer said: "I'm not going to get into speculation about what we would undertake in case the checks were to stop ... for the moment our indications are that the checks are ongoing."
Meanwhile, a senior official at Stormont's Department of Agriculture is seeking legal advice over the issue.
Mr Poots, whose officials are responsible for carrying out Northern Ireland Protocol checks, issued a similar instruction last year, but the checks continued after civil servants were told they were legally obliged to carry them out.
Speaking at Stormont, he said he had received legal advice, which stated that he could order a halt to Northern Ireland Protocol checks.
"The advice concluded that I can direct the checks to cease in the absence of Executive approval," he said.
Mr Poots said he has issued a formal instruction to his permanent secretary to halt all checks that were not in place on 31 December 2020.
The British government has said checks on agri-food coming into Northern Ireland from Britain were a matter for the Stormont executive.
"The operation of checks is a matter for the Northern Ireland Executive," A British government spokesperson said.
The Minister for Foreign Affairs described the move as "unhelpful" and added to the uncertainty for businesses in Northern Ireland.
Speaking on RTE's News at One, Simon Coveney said: "This is a serious issue, but I don't think we should allow it to distract us away from the positive discussions that are taking place between Liz Truss and Maroš Šefčovič, where there is some progress being made."
He confirmed that sanitary and phytosanitary (SPS) checks continue to take place today and said the obligation to fulfil the commitments of the Protocol is "with the British government, primarily".
"The British government signed up to do withdrawal agreements. The protocol is a big part of that."
Additional reporting: Vincent Kearney, Conor Macauley, PA