The Northern Ireland Protocol is the only way to protect the Good Friday Agreement, a senior European Commission official has said.

Maros Sefcovic expressed concerns over “teething problems” over the implementation of the protocol but said it was now “our mutually agreed legal obligation”.

The commission’s vice president made the remarks in a letter to Cabinet Office Minister Michael Gove on Wednesday.

The pair will meet in London on Thursday to discuss the problems faced in Northern Ireland as a result of the new trading arrangements.

It comes amid tensions after the brief triggering by the bloc of Article 16, with particular ire among unionists in Northern Ireland who are calling for it to be ditched.

The protocol was designed to prevent a hard border with Ireland but has resulted in additional checks for goods crossing from Great Britain to Northern Ireland.

Article 16 overrides part of the protocol which prevents a hard border on the island of Ireland, and was intended as an emergency measure only.

Unionists regard the new checks as a border in the Irish Sea separating Northern Ireland from the rest of the UK.

Northern Ireland’s First Minister Arlene Foster has urged Mr Gove and Boris Johnson to “act on” their unionist beliefs.

“I believe they are both unionists but it is important that they act on that now and it is important that they realise that part of the United Kingdom is being treated differently,” she told Peston.

“And actually if you look at the protocol it talks about respecting the fact that the sovereign territory of the United Kingdom as one, it also talks about respecting the internal market of the United Kingdom.

“I don’t believe that the European Union is doing either of those things and so I believe it is up to our Government to challenge them on that and the fact that they are separating out Northern Ireland from the rest of the United Kingdom.”

Mrs Foster said the issues with the protocol are “fundamental”, adding: “You can’t even get a pot plant from Great Britain into Northern Ireland at the moment which is absolutely incredible.”

UUP leader Steve Aiken said the letter “reeks of arrogance and intransigence”.

“Instead of protecting the Belfast Agreement and defusing tensions, this letter will do the exact opposite,” he said.

European Commission president Ursula von der Leyen earlier apologised for “mistakes” that led to the triggering of Article 16.

Our shared objective is to work tirelessly in order to make the protocol work. It requires full and faithful implementation by both parties

However Mr Sefcovic has made it clear in his letter that the commission regards the protocol as the only way forward.

“The protocol is the solution agreed by the UK and the EU to these challenges: it is the only way to protect the Good Friday (Belfast) Agreement, preserving peace and stability and avoiding a hard border on the island of Ireland,” he wrote.

“It is designed to ensure clarity and predictability for people and businesses, while minimising the disruption inevitably caused by the withdrawal of the United Kingdom from the European Union. It is a balanced outcome after years of difficult negotiations and is now our mutually agreed legal obligation.

“I therefore agree that our shared objective is to work tirelessly in order to make the protocol work. It requires full and faithful implementation by both parties.

“The Union’s commitment to the objectives of the protocol on Ireland/Northern Ireland, as a cornerstone of both the Withdrawal Agreement and the relationship between the European Union and the United Kingdom, is unwavering.”

Mr Sefcovic set out concerns over the implementation of the protocol, writing that Border Control Posts (BCPs) are not yet fully operational and official controls not performed in compliance with the Withdrawal Agreement protocol and European Union rules.

He also said the UK has “not yet fulfilled its obligation” to provide real-time access to all its IT systems, in particular access to key customs IT systems.

However, he wrote, he is convinced these are “teething problems, for which we should be able to find swift solutions”.

A UK government spokesperson said: “It is disappointing that the Commission has failed to acknowledge the shock and anger felt right 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.

“The Chancellor of the Duchy of Lancaster will underline the need for such action and political leadership in this regard when meeting with Vice-President Sefcovic in London tomorrow.”