The criticism came ahead of crisis talks between the two sides in London, which drew to a close with both sides reiterating their commitment to “the proper implementation” of the protocol.
Michael Gove was expected in the meeting to request a two-year delay to further checks on food supplies – a suggestion the EU side had been expected to turn down.
A joint statement said Mr Gove and the European Commission’s vice president Maros Sefcovic had had a “frank but constructive discussion” on Thursday evening, in which they agreed to “spare no effort” in implementing solutions.
The two politicians agreed to convene the joint committee no later than 24 February to provide “the necessary political steer” and approval to this work “in the spirit of collaboration, responsibility and pragmatism”.
Irish foreign affairs minister Simon Coveney described the meeting as a “good day’s work”, tweeting: “Focus now is on EU/UK cooperation to implement what’s been agreed in Protocol and to work on solutions to outstanding issues linked to implementation.”
But the cordial statement was preceded by stern words from across the channel. Speaking ahead of the meeting, Mr Barnier said: “The difficulties on the island of Ireland are caused by Brexit, not by the Protocol,” adding that “the Protocol is the solution”.
And, on the blizzard of new red tape for all post-Brexit trade, the chief Brexit negotiator added: “Many of these consequences have not been correctly explained, they have been generally underestimated.”
“Brexit means Brexit,” he told a European Business Summit event, stealing the slogan coined by Theresa May, when she sought hard exit terms.
While there could be “technical solutions” for some of the problems becoming apparent, the Brexit negotiations were over and the rules must be respected, he added.
The comments came as the Irish prime minister, Micheal Martin, called for both sides to “dial down the rhetoric”, warning Ireland risked being “collateral damage” in the row.
Many EU leaders are angry that the UK appears to be exploiting the controversy over its brief triggering of border controls in Ireland – over coronavirus vaccine exports – to try to overturn the protocol.
Keir Starmer also called for cool heads from both sides in approaching issues around Northern Ireland, saying: “There is increasing tension that needs to be de-escalated.”
A day before their meeting, Mr Sefcovic was accused of inflaming tensions between the UK and EU in a response to Mr Gove's claim, made on Monday, that the protocol was "not working" and needed changes.
In a letter, Mr Sefcovic questioned why border control posts at ports in Northern Ireland were “not yet fully operational” six weeks after Brexit was completed.
There were “very few identity checks” on goods, while “non-compliant consignments” were being accepted even if destined for the Irish Republic, he wrote.
Goods were entering Northern Ireland “without being declared or without valid certificates”, and the UK had “not fulfilled its obligation” to allow the EU real-time access to customs IT systems.
On the UK's call for a two-year extension to "grace periods", Mr Sefcovic wrote that changes “cannot be agreed beyond what the protocol foresees already”.
Boris Johnson’s spokesperson called the response “disappointing”, explicitly linking its call for a rethink to the row over the EU’s aborted invocation of Article 16, which allows part of the protocol to be overridden – and is meant to be used only in emergencies. The bloc imposed the temporary change in a row over coronavirus vaccines.
“The commission has failed to acknowledge the shock and anger felt across the community in Northern Ireland from its decision to trigger Article 16 and the need to take urgent steps to restore confidence as a result,” he said.
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