Ursula von der Leyen has expressed regret for creating a row with the UK last month.
The EU’s top official said that mistakes were made when the bloc briefly considered applying an emergency restriction on exports of Covid-19 vaccines also to Northern Ireland.
The EU introduced tighter rules on exports of vaccines that could have hit shipments to nations like the UK amid a dispute with Anglo/Swedish pharmaceutical firm AstraZeneca.
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To implement its plan, EU officials thought about also introducing controls on exports to Northern Ireland from Ireland – creating a hard border.
As a result, the plans sparked outrage and a political row erupted since the Brexit deal guarantees that goods flow freely between the EU and Northern Ireland to protect the Irish peace process.
The EU reversed its decision amid the outcry.
Speaking at the European Parliament on Wednesday, European Commission president Ursula von der Leyen said she was sorry for the confusion.
“The bottom line is that mistakes were made in the process leading up to the decision,” Ms von der Leyen said.
“And I deeply regret that. But in the end we got it right.”
Ms Von der Leyen was speaking a day after Britain’s chief Brexit minister said that relations between the United Kingdom and the EU had suffered from turbulence since their economic divorce six weeks ago.
The UK left the EU politically just over a year ago, and quit the bloc’s economic structures on December 31.
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Since then, customs and veterinary checks have been imposed on goods moving between Britain and EU member nations – and on some British goods going to Northern Ireland because it shares a border with Ireland.
The checks have unsettled the delicate political balance in Northern Ireland.
The new measures are opposed by pro-British unionists, who say they drive a wedge between Northern Ireland and the rest of the UK.
Northern Ireland authorities halted veterinary checks and withdrew border staff from ports for several days this month after threatening graffiti appeared referring to port workers as targets.
Ms Von der Leyen added that the EU’s executive arm would do its “utmost to protect the peace of Northern Ireland, just as it has done through the entire Brexit process”.