Europe’s dramatic decision to impose export controls on vaccine manufacturers could impact the rollout of the jab in Australia, after the country was left off a list of nations exempt from the new restrictions.

Overnight on Friday the European Union set off a global diplomatic row when it went ahead with a threat to impose sweeping powers allowing it to block Covid-19 vaccine shipments from the bloc.

The decision, which had been telegraphed by the European Commission, was made a week after pharmaceutical giant AstraZeneca revealed it would cut deliveries of its vaccine to Europe by 60% in the first quarter due to production problems at a factory in Belgium.

The shortfall has prompted a tense diplomatic spat between Brussels and the UK. Europe had expressed concern that doses meant for the continent might be shipped to the UK, where AstraZeneca is based.

The EU had also called for vaccine doses at two sites in the UK to be made available to European citizens, a request the company said it could not fulfil because of the terms of its contract with Britain.

In response, the commission announced on Friday that it would tighten the export rules of shots produced in the 27 EU countries.

“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.”

The “vaccine export transparency mechanism” would be used until the end of March and would control shipments to non-EU countries and ensure any exporting company based in the EU first submits its plans to national authorities.

The decision has been roundly criticised, including by the World Health Organisation’s director-general Tedros Adhanom Ghebreyesus, who told a virtual briefing that “hoarding vaccines” would “keep the pandemic burning”.

“If we hoard vaccines and we are not sharing, there will be three major problems. One, I have said it, it will be a catastrophic moral failure and two it keeps the pandemic burning and three very slow global economy recovery,” he said.

The decision has the potential to have a damaging impact on Australia’s own supply of vaccine doses.

Although the vast bulk of the AstraZeneca vaccine doses bought by Australia are being produced domestically by partner company CSL, the company had been due to import 3.8 million doses from Europe. This week the health minister, Greg Hunt, was forced to concede the government had now been forced to cut that back to 1.2m doses.

But it could also impact the supply of Pfizer’s vaccine, currently the only company to have secured the approval of Australia’s Therapeutic Goods Administration. Pfizer is due to begin sending about 80,000 doses per week from Belgium to Australia from next month.

The full extent of the decision is not yet clear, but the EU’s decision to leave Australia off a list of more than 120 countries exempted from the new regulations will mean the two pharmaceutical companies will need to seek approval to make shipments to the country.

Speaking before the EU formalised the decision at a Senate hearing this week, Pfizer’s Australia and New Zealand medical director, Krishan Thiru, said the company would consider moving production of its vaccines to another country.

“Should that happen we will explore what options are available,” Thiru said. “We have large scale of manufacturing across the US and ­Europe. No ­determination has been made at this point in time about switching the source of our manufacture of vaccinations.”

The government in Australia had not publicly responded to the EU’s decision by noon on Saturday. On Friday, the Australian health minister, Greg Hunt, confirmed Australia would seek “certainty” for Australia’s vaccine supplies from both the WHO and EU.

“We understand the whole world has to deal with supply shocks and therefore our volumes have been appropriately set out this week,” Hunt said on Friday.

“But the foreign minister has confirmed today that Australia will be making representations through the World Health Organisation and through Europe, with regards to ensuring that the vaccine supplies and certainty for Australia.”

On Saturday the veterans affairs minister, Darren Chester, confirmed that the foreign affairs minister, Marise Payne, was raising the issue.

“Now, as we understand our situation here in Australia, right now we are on track, we have brought forward the approval process, it’s been fully approved in terms of distribution of the vaccine we expect to roll out towards the end of February,” Chester told ABC News.

“These supply shocks were not unexpected given the nature of the virus.”