Brussels has retreated from an incendiary plan that would have created border restrictions between the Irish Republic and Northern Ireland as part of its efforts to clamp down on vaccine exports from the EU.

Politicians in Dublin, London and Belfast had expressed alarm over the European Commission’s decision to trigger an override mechanism in the Northern Ireland protocol to the Brexit treaty — just weeks after the UK’s departure from the single market.

In a statement late on Friday, the commission said it would now be ensuring the protocol is “unaffected” by its proposed vaccine export control measures which form part of its efforts to contend with a shortage of jabs in the bloc.

Earlier, the export proposals had been taken down from the commission’s website just hours after publication, as top officials in Dublin, London and Brussels conducted frantic diplomacy.

The volte face is an acute embarrassment for the commission and its president Ursula von der Leyen. It follows a week of turmoil for Brussels, as it battles a severe supply squeeze in the EU’s vaccine rollout and fights AstraZeneca over a shortfall in deliveries of the company’s jabs.

The commission had announced the Irish border action as part of tighter vaccine export controls that would allow EU member states to block sales of vaccines to countries such as the UK, US and Japan.

But the provisions affecting Northern Ireland immediately triggered a wave of anxiety across the political spectrum in the UK and Ireland.

Irish prime minister Micheál Martin raised the matter directly with Ms von der Leyen. Boris Johnson, UK premier, spoke with both leaders and told Ms von der Leyen of his “grave concerns”, the UK government said.

Michael Gove, UK Cabinet Office minister, called commission vice-president Maros Sefcovic to express concern over a lack of notification from the EU, saying the UK was “considering its next steps”.

Arlene Foster, Northern Ireland’s first minister, condemned the commission’s original move as an “incredible act of hostility”. Brussels had “at the first opportunity” placed a hard border between the region and the Irish Republic over a vaccine supply chain, she said.

Arancha Gonzales, Spain's foreign minister, called the initial attempt to use the restrictions in this way an “accident”. “The mishap has been repaired,” she told the BBC's Newsnight.

Ireland immediately welcomed the climbdown. Mr Martin said the shift by the commisison was a “positive development” in light of the challenges presented by the pandemic. On Twitter the taoiseach cast the move as a “welcome decision” following what he described as “constructive discussions” with Ms von der Leyen.

In its statement on Friday the commission said it would be publishing a revised version of the regulation on Saturday morning.

The rules will require that vaccine exports are subject to authorisation by member states. “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,” the commission warned.

The new EU export rules do not explicitly target the UK but the language used echoes Brussels’ concerns that vaccines made in the European bloc have been shipped across the Channel — and could be again.

The initial version of the regulations refers to EU delivery shortfalls by “certain vaccine manufacturers” — an apparent reference to the spat between AstraZeneca and the commission, where officials have questioned whether supplies have been sent to the UK.

The EU wants AstraZeneca to divert production from its UK plants to make up for an expected shortfall of deliveries to the bloc and on Friday published details of its contract with the UK-headquartered company.

But Mr Johnson remains convinced the UK’s contract with AstraZeneca — signed last June, three months before the EU deal — is watertight and will guarantee that UK production is used to meet the company’s promise to deliver 100m doses.

AstraZeneca’s jab was on Friday cleared for use in EU by the bloc’s medical regulator.

The European Medicines Agency said it backed the Oxford/AstraZeneca jab for all individuals aged 18 and over, even as Germany and France expressed concern over its effectiveness for those aged 65 and over.

Hours before the EMA decision, French president Emmanuel Macron said: “Today everything suggests that [the Oxford/AstraZeneca vaccine] is almost ineffective for those over 65, and some say over 60.”

France on Friday tightened its coronavirus restrictions, closing its borders for arrivals from outside the EU from Sunday except for “essential reasons”. It also shut shopping malls from the same day, without imposing a full new lockdown.

Additional reporting by Victor Mallet in Paris