A dispute broke out in January 2021 between the European Commission and the pharmaceutical company AstraZeneca AB about the provision of COVID-19 vaccines during the COVID-19 pandemic, and, in February, spilled out into a dispute over Article 16 of the Northern Ireland Protocol. Vaccination proceeded apace in the UK but more slowly in the EU, and by the end of March 2021, over 30% of the UK population had received at least one dose of vaccine compared to about 8% of the EU population. This was partly due to limited availability of the AstraZeneca vaccine in the EU. The World Health Organization and the European Medicines Agency continued to state that the vaccine was safe and effective. However, a representative of the European Medicines Agency said in June that vaccines based on the mRNA technology should be preferred if available for all age groups, including for the over 60s.

Background In anticipation that a successful vaccine against COVID-19 would be developed, various countries pre-ordered doses of vaccine from the organisations doing research. The United Kingdom pre-ordered 100 million doses of the Oxford–AstraZeneca COVID-19 vaccine candidate by May 2020, through AstraZeneca UK Limited. While in parallel offering UK taxpayer-funded grants to vaccine manufacturers, in the UK and EU, to increase capacity, including approximately £21 million of UK funding for the Halix plant in the Netherlands, according to a report in the Daily Telegraph. in advance of the clinical trials of the Oxford vaccine candidate. The EU denied that the Halix plant had received any UK government funding. The US Government, and WHO COVAX programme placed similar conditional pre-orders, for 600 million doses of the Oxford vaccine candidate, in the following weeks, with the US administration offering $1.2 bn in funding for development, and clinical trials of the candidate. The EU made a 336 million euro downpayment to Astrazeneca in August to cover development, liability and other costs incurred by the vaccine maker. The Swedish subsidiary, AstraZeneca AB, reached a preliminary agreement, on 13 June, with the short lived Inclusive Vaccines Alliance, a group made up of France, Germany, Italy and the Netherlands, to supply up to 400million doses for the club of four. This Inclusive Vaccine Alliance was meant as the first step towards a collaborative EU approach to vaccine procurement, and subsequently the national health ministers mandated the EU commission to take over. In the past, the European Union member states had decided on their own health policies, but during the summer of 2020, Brussels therefore took charge of vaccine procurement in what Ursula von der Leyen called a "European Health Union". Member states could opt out of this, from the centralised EU procurement process, but none initially did, except for Hungary. Negotiating on behalf of the whole EU, the European Commission signed a deal with AstraZeneca AB, on 27 August 2020.

The European Union was generally slow in signing their vaccine contracts because they were demanding producer liability if something goes wrong and wanted to conduct a rolling-review process (leading to ordinary regulatory approval) rather than an emergency authorisation. The priority of the European Medicines Agency and of the individual member states was not speed but to build public confidence in the safety of the vaccines and the mass vaccination process. However, the European governments conceded some immunity to AstraZeneca and to pay potential claims above an agreed limit, and this was different from the contract they made, for example, with EU-based Sanofi.

An analysis by Isaac and Deutsch in Politico Europe indicate the UK involvement began with a £65 million grant to Oxford University in April 2020 to develop a production plan for their vaccine which evolved into a binding agreement in May 2020 with AstraZeneca UK Limited. This agreement related to UK supply and became the basis for the formal UK contract signed on 28 August 2020, a day after the EU contract, with the Swedish subsidiary. The contract with the UK subsidiary differs from the EU Contract, with the Swedish subsidiary, in that the UK contract is under English law, rather than the Belgium law specified in the EU contract, and having more specific details on key points that relate to interruptions in UK supply. The two contracts with the EU and the UK both included ″best effort″ clauses.

When the Oxford–AstraZeneca vaccine was approved for use in the United Kingdom on 30 December 2020, vaccinations began to be rolled out. It was the second vaccine to enter the national rollout programme, joining the Pfizer–BioNTech vaccine which had been approved on 2 December 2020. AstraZeneca submitted its application for conditional marketing authorisation to the European Medicines Agency (EMA) on 12 January 2021, EMA subsequently approved the use of the Oxford–AstraZeneca vaccine on 29 January, joining the Pfizer vaccine, approved on 21 December 2020, and the Moderna vaccine on 6 January 2021. Hours earlier, French president Emmanuel Macron had stated that the Oxford–AstraZeneca vaccine was "quasi-ineffective for people over 65". EMA recommended its use for anyone from age 18, but cautioned that efficacy for over 55s was likely but remained unknown at the time. Some national regulators therefore restricted its use for the elderly. For example, the German Standing Committee on Vaccination (STIKO) did not recommend the use for over 65s at the time because AstraZeneca had not submitted data which showed efficacy for this age group, adding that ″when there is more and better data, STIKO will change its recommendation″. By the end of January, two per cent of the population of the European Union had received the first of the required two vaccines shots compared with around ten per cent in the United Kingdom. The UK decided to have an emergency approval rather than regular approval (which holds manufacturers to account should something go wrong) and to trust in just-in-time delivery rather than to stockpile second doses as most EU members states did, according to an analysis in Deutsche Welle. Most EU member states opted to provide the second dose at the earliest opportunity. They also wanted to avoid harmful rivalries between member states and a heterogeneous vaccination rate in order to minimise the risk of mutated strains adapting to the vaccine.

According to investigative research by Der Spiegel, the Oxford University developers first sought to collaborate with the US firm Merck because of its experience in vaccine production. However, because of US President Donald Trump's America First policies and the concern that any collaboration with a US company would mean that the US is served first, British health minister Matt Hancock intervened. While the UK was in the process of leaving the European Union, Hancock explained on radio station LBC that he did not want to sign a contract that would require the Oxford vaccine to be delivered to other countries before the UK. As a result, AstraZeneca became Oxford's partner in April 2020, even though AstraZeneca had no previous experience in vaccine research. Der Spiegel argued that this might explain why the regulatory agencies found flaws in the data submitted and why the company had underestimated the production difficulties and overstated their production capacities. AstraZeneca's CEO Pascal Soriot assured the Johnson government that it would supply a large share of the vaccine early and exclusively to the UK. In return, the British task force set up for vaccine procurement pledged the participation of hundreds of thousands of volunteers in clinical trials and the generous assumption of liability risks, an offer that no pharmaceutical company could turn down, according to Der Spiegel.

January dispute In the third week of January 2021, AstraZeneca announced that problems at the Belgian plant where it produced the vaccine would reduce the supply available to the European Union from the 80 million doses expected by the end of March, to 31 million doses. This news came at a time when Pfizer had also reduced the output of its vaccine to allow for an upgrade of its facilities. This left the European Union with a shortfall on its requirements. On 25 January, Stella Kyriakides, Europe's health commissioner, stated that discussions were taking place with AstraZeneca, but that the company had not given satisfactory answers as to which doses had been manufactured and to whom they had been delivered. The company responded by stating that its contract with the United Kingdom gave that nation the first claim to vaccines produced domestically, whereas its contract with the European Union only required it to make its "best reasonable efforts" to deliver the doses on time. The contract with the UK included multiple, similar "reasonable best efforts" clauses, for AstraZeneca UK Limited, and any sub-contractors employed. Both the EU and UK contracts were subsequently published. The EU commission also had AstraZeneca's Belgian plant inspected and found that this plant had produced all the doses it was obliged to under its contract with AstraZeneca.

The Northern Ireland Protocol of the Brexit deal guarantees free movement of goods on the border between Northern Ireland and the Republic of Ireland. On 29 January, the European Commission published a draft of its export transparency mechanism (a form of export control) to gain oversight of the movement of vaccines. This included reference to the possible use of Article 16 of the Northern Ireland Protocol in introducing export controls, to prevent supplies of vaccine aimed at the Republic of Ireland moving to the rest of the UK via Northern Ireland. Article 16 allows limited unilateral deviation from the Protocol, subject to various criteria being met. This move was criticised in Northern Ireland, the Republic of Ireland and the UK, with the first minister of Northern Ireland, Arlene Foster, stating it was "an absolutely incredible act of hostility". The EU reversed the decision the following day acknowledging that a mistake had been made.

However, the EU introduced export controls on coronavirus vaccines made inside the bloc. They had to be approved by national governments, unless they are destined for the Covax mechanism to supply the poorest countries or for a number of European states not in the EU. The World Health Organization criticised this move as likely to prolong the pandemic and slow economic recovery around the world. The European Union's chief Brexit negotiator, Michel Barnier, asked the Commission to step back from the deepening row.

Later, on 29 January, the UK was left off a list of 120 countries to which vaccines could be exported freely. Instead, manufacturers in the EU must notify national authorities before exporting vaccines to any country not on the list. The authorities have the right to refuse to allow the export if they consider that doing so would jeopardise the supply of vaccines to the EU. The new measures meant that vaccines from AstraZeneca plants in the EU might be prevented from being exported to the UK. This mechanism raised fears that Pfizer-Biontech, which also makes vaccines in the EU, might be at risk of export bans if there are supply problems.