Just weeks after the UK finally completed its departure from the EU, the topic that dogged more than four years of bitter wrangling over Brexit has reared its head again: the tortured question of the Irish border.

During the past few days ministers and officials from the European Commission and the UK have been trying to ease growing tensions over the so-called Northern Ireland protocol — the part of Boris Johnson’s Brexit treaty designed to avoid a hard border on the island of Ireland. Talks will continue in London next week.

The catalyst for the latest row was last Friday’s “mistake” by the commission when it triggered emergency protocol provisions to prevent coronavirus vaccine exports to Northern Ireland so they could not be sent on to Britain — in effect creating a land border with the republic.

“The mood here is that we messed up. We made a blunder. We handed an advantage to the other side,” said a senior Brussels figure.

The move to invoke the emergency override part of the agreement — Article 16 of the protocol — made without consultation, was swiftly reversed after a storm of protest from London, Dublin and both sides of the historic political divide in Belfast. But the fallout from the decision left many asking whether the protocol in its current form can survive.

In a letter sent to the commission on Wednesday Michael Gove, the UK’s Cabinet Office minister, called for an “urgent reset” of the protocol. Mr Johnson’s earlier threat to trigger Article 16 had already raised the temperature.

Maros Sefcovic, the European Commission vice-president, pushed back hard on Thursday, calling on Britain to focus on “proper implementation” of the new regime rather than suspending it outright.

Two European officials with knowledge of internal discussions said the commission’s mistake last week did not justify the UK’s extensive demands.

Mr Gove has called for 18-month extensions to existing grace periods, some of which lapse on March 31 and the most pressing of which is a crucial waiver on food retailers needing to fill out export health certificates.

“We are aware of the difficulties on the ground as a result of the UK becoming a third country on January 1,” one senior EU diplomat warned.

“But let’s separate that from a Covid-related policy mistake of last Friday. To use last Friday to change the [Brexit agreement] is not a very long term strategic way of thinking.”

Mr Sefcovic told MEPs at a closed-door meeting on Thursday that Brussels was “concerned” by the request to prolong the grace periods, said officials present at the meeting. The commissioner also listed a series of areas where the UK has so far not delivered on its promises under the protocol, including the establishment of trusted trader schemes and data sharing access for customs databases.

Despite some taking a hard line in Brussels, one senior figure said: “There has to be a degree of willingness to make this work, not so much compromise as willingness to be flexible going forward. [The protocol] has to survive and will survive.”

Ireland, which would suffer severe fallout from a breakdown in EU-UK relations, signalled support for “sensible, common sense modifications” to the operation of the protocol. “It does need some changes,” Micheál Martin, premier, said this week.

There is deep frustration on the UK side over the EU’s dogmatic approach. British officials argue that Brussels now risks destroying arrangements to which the UK remains fundamentally committed even though they appear difficult to justify given Northern Ireland’s place in the UK internal market.

The row has emboldened Northern Ireland’s pro-UK unionists who were humiliated by Mr Johnson when he agreed to an Irish Sea regulatory border as the price for an orderly divorce from the EU in 2019. After rejecting the arrangement as an affront to their British identity, they looked on in horror in the new year as new red tape led to empty shop shelves as supplies of hundreds of products ran out.

The Northern Ireland Retail Consortium, which represents large supermarket chains, said the situation has improved as traders become accustomed to new procedures. “We are coping,” said Aodhán Connolly, the NIRC’s director, who is pushing to extend grace periods. UK supermarkets have warned the protocol will become “unworkable” without such moves.

“The word of 2020 was ‘sovereignty’. The word in 2021 needs to be ‘simplification’,” Mr Connolly added.

The new system has proved a nightmare for smaller businesses. “With all the paperwork GB companies are refusing to deliver to us,” said Kieran Sloan, owner of Sawers high-end delicatessen in central Belfast, which has traded for more than a century.

There have been numerous other examples of disruption: garden centres unable to source seeds and potted plants from Britain; shipments of agricultural machinery delayed because of soil on wheels; and frantic talks to avert a stoppage of steel deliveries.

This is the backdrop to mounting unionist pressure on Arlene Foster, the Democratic Unionist first minister of the region, to adopt a more assertive political stance.

Her calls to maximise the opportunities from the protocol definitively ended this week as she called for Northern Ireland to be “freed” from the arrangement and withdrew her party’s political co-operation.

“In terms of the DUP, I think they have been very very spooked,” said Alex Kane, a commentator who formerly worked for the rival Ulster Unionist party.

Brexit checks on food and animal products at the region’s biggest ports in Belfast and Larne were suspended on Tuesday because of intimidation of officials. Although the Police Service of Northern Ireland points to “considerable tension” among hardline unionists, it said there was “absolutely no information to substantiate or corroborate” claims that outlawed pro-British loyalist paramilitaries were involved in the threats. The port inspections had still not resumed on Thursday.

Katy Hayward, from Queen’s University Belfast, said concerns in the region about the protocol were genuine.

“To make it work, you have to strengthen the middle ground of undramatic pragmatism,” Prof Hayward said.

“But there are many things that work against the protocol, including the fact that the British government was never that honest about what it signed up to, which has enabled the DUP to cling to the delusion that it might not mean a border in the Irish Sea.”

Additional reporting: Michael Peel in Brussels