The European Union has backed down on its threat to override part of the Brexit deal on Northern Ireland after widespread condemnation of the move as part of its export controls on coronavirus vaccines.

Boris Johnson had warned European Commission president Ursula von der Leyen of his “grave concerns” over Brussels’ move to invoke Article 16 of the Northern Ireland Protocol to stop the unimpeded flow of jabs from the bloc into the region on Friday.

But an EU source told the PA news agency the move had been a “misjudgment”, as the European Commission U-turned to say it is “not triggering the safeguard clause” to ensure the protocol is “unaffected”.

The move to impinge on the protocol, which blindsided both the UK and Ireland and provoked condemnation from across the political spectrum, came as the bloc is embroiled in a row with pharmaceutical giant AstraZeneca over shortfalls in the delivery of jabs.

Northern Ireland’s First Minister Arlene Foster described Brussels’ initial move as an “incredible act of hostility” that places a “hard border” between the region and the Republic of Ireland.

But after Irish premier Micheal Martin and the Prime Minister both held calls with Ms von der Leyen, the commission issued a statement to back down on Article 16, a move it earlier justified over a lack of vaccine supplies.

“In the process of finalisation of this measure, the commission will ensure that the Ireland/Northern Ireland Protocol is unaffected. The commission is not triggering the safeguard clause,” the statement said.

But it continued to threaten further action, saying: “Should transits of vaccines and active substances toward third countries be abused to circumvent the effects of the authorisation system, the EU will consider using all the instruments at its disposal.”

Ms von der Leyen said she spoke to Mr Martin to “agree on a satisfactory way to introduce an export authorisation mechanism” for vaccines.

And she said she had held “constructive talks” with Mr Johnson, adding: “We agreed on the principle that there should not be restrictions on the export of vaccines by companies where they are fulfilling contractual responsibilities.”

Irish foreign affairs minister Simon Coveney demanded “lessons should be learned” and warned the protocol “is not something to be tampered with lightly, it’s an essential, hard won compromise, protecting peace and trade for many”.

Spanish foreign minister Arancha Gonzalez-Laya told BBC Newsnight: “I understand, and this is what I hear from the European Commission, that there was an accident.”

The Taoiseach, who welcomed the U-turn, held multiple calls with Ms von der Leyen, and PA understands that Mr Martin was not given advance notice of Brussels’ decision to invoke the protocol.

Mr Johnson also spoke to the EU chief, as Downing Street warned the bloc not to disrupt the supply of jabs.

“He expressed his grave concerns about the potential impact which the steps the EU has taken today on vaccine exports could have,” a No 10 spokesman said.

In a flurry of diplomacy, Mr Martin and the Prime Minister also discussed their concerns, with Mr Johnson urging the EU to “urgently clarify its intentions and what steps it plans to take to ensure its own commitments with regards to Northern Ireland are fully honoured”.

A Downing Street statement added: “The UK has legally-binding agreements with vaccine suppliers and it would not expect the EU, as a friend and ally, to do anything to disrupt the fulfilment of these contracts.”

The protocol, which is part of the Withdrawal Agreement, is designed to allow the free movement of goods from the EU into Northern Ireland, and prevent the need for a hard border on the island of Ireland.

But triggering Article 16 would have temporarily placed export controls on the movement of vaccines, a move that was threatened by the EU to prevent Northern Ireland being used as a back door to move coronavirus vaccines from the bloc into the UK.

The European Commission’s new regulation had stated: “This is justified as a safeguard measure pursuant to Article 16 of that protocol in order to avert serious societal difficulties due to a lack of supply threatening to disturb the orderly implementation of the vaccination campaigns in the member states.”

In an interview with The Times, EU chief Brexit negotiator Michel Barnier urged Brussels to step back from the vaccine row as he called for a “spirit of co-operation” during the “extraordinarily serious crisis”.

“And I believe that we must face this crisis with responsibility, certainly not with the spirit of oneupmanship or unhealthy competition,” he added.

Regardless of the protocol U-turn, preventing vaccines made within the EU from being exported could hinder the UK’s access to further supplies, particularly to the Belgian-made Pfizer jab.

Brussels has also demanded doses of the AstraZeneca vaccine manufactured in British plants in order to solve its supply shortage issues, as member states were forced to pause or delay their rollouts.

The EU’s “vaccine export transparency mechanism” will be used until the end of March to control vaccine shipments to nations outside the bloc.

It seeks to ensure that any exporting company based in the EU first submits its plans to national authorities.

The UK was not named among countries exempted from the new measures.

Meanwhile, AstraZeneca published a redacted version of its contract with the EU, which the bloc said was important for “accountability”.

The contract mentions that the firm would use “best reasonable efforts” to use European plants, including two in the UK, as production sites for vaccines destined for the EU.