The EU also abruptly reversed course on a plan to use emergency Brexit measures to restrict exports of vaccines through the Irish border to the United Kingdom after it sent shockwaves through Belfast, London and Dublin.
The European Commission has launched a scheme to monitor and in some cases bar exports of vaccines produced in EU plants, amid a row with British-Swedish drugs giant AstraZeneca.
The move was firmly criticised by the World Health Organization and risked stoking conflict with the UK just weeks after London and Brussels sealed a trade deal.
"We paid these companies to increase production and now we expect them to deliver," EU Commission vice-president Valdis Dombrovskis told reporters.
"Today's measure has been adopted with the utmost urgency. The aim is to provide us immediately with full transparency.... And if needed, it also will provide us with a tool to ensure vaccine deliveries."
EU officials said they expected the order to come into effect on Saturday after its publication in the official journal.
The emergency measure is initially for six weeks but is intended to then continue until at least the end of March.
The WHO said the move was part of a "very worrying trend" that could jeopardise the global supply chain for vaccines.
"It is not helpful to have any country at this stage putting export bans or export barriers that will not allow for the free movement of the necessary ingredients that will make vaccines, diagnostics and other medicines available to all the world," said Mariangela Simao, WHO assistant director for access to medicines and health product.
The EU's plan applies only to those coronavirus vaccines that are covered by advance purchase agreements between drug companies and the European Commission.
Those firms in the EU will have to apply for an authorisation to export doses meant for countries outside the bloc, and show their export records for the previous three months.
A response would normally be given within 48 hours, though that could be extended if necessary.
Most non-EU countries in and around Europe, such as Switzerland, those in the Balkans or micro-states like Monaco, are exempted from the measure.
But Britain, which last year left the EU amid much acrimony, is not.
Brussels has been in a furious dispute with AstraZeneca this week, accusing it of breaching its contract by delaying deliveries to EU governments while maintaining those under a deal it signed earlier with the UK.
But Health Commissioner Stella Kyriakides insisted: "We are not protecting ourselves against any specific country. And we're not in competition or in a race against any country."
The prior three-month reporting period would presumably reveal whether or not AstraZeneca did indeed – as has been alleged – send vaccines to Britain from its vaccine plants in Europe, which it says have since been hit by production glitches.
Belgian authorities on Thursday searched one AstraZeneca plant in southern Belgium at the European Commission's request. Data seized is being analysed.
EU officials insisted that the scheme is not targeting AstraZeneca alone, but all Covid vaccine-exporting firms tied to the Commission by contracts.
The main goal, they said, was to gather information, though they admitted that in "certain circumstances" vaccine exports could be denied.
"What we want to achieve is of course, a fair approach. And transparency will help us in that respect," said one official on condition of anonymity.
The officials noted that the EU's vaccine procurement portfolio is for 2.5 billion doses of authorised and potential vaccines – more than enough for the bloc's 450 million inhabitants.
That is because the Commission also bought on behalf of poorer countries, with its excess doses to be funnelled through the WHO-led COVAX facility.
"We're not talking about vaccine nationalism," one official said. "From the beginning we intended to share these vaccines with our neighbours."
Right now, though, the EU's vaccination programme is flagging badly, triggering anger among member states.
Japan's vaccine rollout chief also warned that growing nationalism over supplies of Covid-19 shots could lead to retaliation and disruptions to global supplies.
Taro Kono said he was concerned about the EU announcement that it may block exports of vaccines produced there until sufficient supplies are provided to the European people.
"It is understandable to put their own people first," Kono said during an online panel hosted by the World Economic Forum. "But we are living on the same planet, and the supply chain now goes global."
"It is time for the leaders of the states to sit down and have an online conversation" to address the issue, he added.
READ MORE: Vaccine nationalism to make Covid-19 worse
EU says not suspending Northern Ireland Brexit terms
The EU said it had not triggered a mechanism to control vaccine exports to Northern Ireland included in the Brexit agreement with the UK, after London voiced "grave concerns" over the threatened move.
"In the process of finalisation of this measure, the Commission will ensure that the Ireland / Northern Ireland Protocol is unaffected," the EU Commissioner said in a statement.
"The Commission is not triggering the safeguard clause," they added, which would have allowed the European bloc to impose controls on exports from the EU to Northern Ireland.
The European Union sought to restrict exports of Covid-19 vaccines through the Irish border to the United Kingdom by invoking emergency clauses in the Brexit divorce deal, sending shockwaves through both Ireland and Northern Ireland.
Northern Irish unionists cast the move as an act of hostility while Irish Prime Minister Micheal Martin sought urgent clarification from European Commission President Ursula von der Leyen.