Britain is on a collision course with the EU over vaccine shortages after Brussels refused to accept that people in the UK have first claim on Oxford/AstraZeneca doses produced in local plants.

The EU’s health commissioner outright dismissed on Wednesday an argument made by Pascal Soriot, the Anglo-Swedish company’s chief executive, that he was contractually obliged to supply the UK first.

In a withering statement, Stella Kyriakides said the UK should not earn any advantage from signing a contract with AstraZeneca three months before the EU’s executive branch put pen to paper.

“We reject the logic of first come, first served,” the commissioner said. “That may work in a butcher’s shop but not in contracts and not in our advanced purchase agreements.”AstraZeneca has enraged Brussels and EU capitals by warning that it will be able to deliver only 25% of the doses scheduled for delivery in the first quarter of the year once the European medicines authority has given its approval, as is expected on Friday.

At the same time, the company has assured the British government, which chose not to be part of the EU vaccine programme, that it will fulfil its promise to deliver 2m doses a week for the benefit of UK residents.

On Tuesday UK government sources insisted that only once British facilities had produced 100m doses for the local population would those plants be free to supply other countries.

The EU is investing €336m in AstraZeneca in return for 400m doses of its vaccine, the first 80m of which had been expected before April.

Boris Johnson risked further inflaming matters on Wednesday by claiming it would have been a “great pity” if the UK had followed advice to stay in the EU vaccine programme rather than set up its own plan.

“I do think that we’ve been able to do things differently, and better, in some ways,” the prime minister told the House of Commons. “But it is early days, and it is very, very important to remember that this is an international venture, these vaccines. We depend on our friends and partners, and we will continue … to work with those friends and partners in the EU and beyond.”

AstraZeneca denies report coronavirus vaccine not effective for people over 65 years

The clash between British and European interests, after a year of tense negotiations over post-Brexit trade and security, poses a threat to relations at a time when EU institutions and 27 EU governments are coming under criticism for the slow deployment of their vaccination programmes.

While the UK has administered vaccine first doses to more than 10% of adults and plans to vaccinate the most vulnerable 15 million – including all over-70s – by mid-February, the EU has reached 2% so far. The UK’s regulator approved the Oxford/AstraZeneca vaccine in late December.

Kyriakides said that under its contract with AstraZeneca, four European plants were named as suppliers and two of those were based in the UK, and she expected them to work for EU citizens.

The company has claimed that the contract with the EU only obliges it to make “best efforts” to supply the bloc, in the understanding that it has other obligations, and that the vaccine production process is prone to breakdown.

A spokesperson for AstraZeneca said: “Each supply chain was developed with input and investment from specific countries or international organisations based on the supply agreements, including our agreement with the European commission.

“As each supply chain has been set up to meet the needs of a specific agreement, the vaccine produced from any supply chain is dedicated to the relevant countries or regions and makes use of local manufacturing wherever possible.”

Kyriakides, a Cypriot who studied in Britain, said the argument was unacceptable and the company had a moral duty to treat the EU similarly to the UK.

She said: “We are in a pandemic. We lose people every day. These are not numbers, they’re not statistics. These are persons with families with friends and colleagues that are all affected as well.

“Pharmaceutical companies, vaccine developers have moral, societal and contractual responsibilities, which they need to uphold. The view that the company is not obliged to deliver because we signed a best effort agreement is neither correct, nor is it acceptable.”

Kyriakides said there was no “priority clause” that would justify British residents benefiting first from doses made in the UK.

The European commission is rifling through customs records over fears vaccines made on EU territory have been shipped to the UK. “The customs data do not lie,” a senior EU official said. “You can be assured that we will find the information, that’s for sure.”

Kyriakides said: “No company should be under any illusion that we don’t have the means to understand what is happening.”

The EU has called for AstraZeneca to waive its concerns over confidentiality and publish the vaccine contract. Officials said they would look into whether comments from its chief executive were in breach of its clauses.

In his interview, the French head of AstraZeneca lamented problems in a plant in Belgium but said he was duty-bound to put the UK first.

“The UK agreement was reached in June, three months before the European one,” Soriot said. “As you could imagine, the UK government said the supply coming out of the UK supply chain would go for the UK first. Basically that’s how it is.”

In response to the shortages, the commission is to release details of a new “transparency register” by the end of the week to oblige vaccine suppliers to notify it of exports, with the German government raising the prospect of a block on the movement of doses outside the EU.

The EU wants to ensure that doses made in AstraZeneca’s plants in Belgium and the Netherlands are not in future sent to the UK. There is also the risk that exports of the Pfizer/BioNTech vaccine from European plants could be blocked from reaching the UK, although the commission has sought to assuage those fears.