Boris Johnson has raised the stakes in a bitter dispute with Brussels over post-Brexit rules in Northern Ireland, warning he could invoke emergency measures to ensure there was no “barrier of any kind in the Irish Sea”.

Mr Johnson told MPs on Wednesday he would legislate if necessary or use emergency override powers — Article 16 in the Northern Ireland protocol, which forms part of the UK’s 2019 Brexit treaty with Brussels — to maintain the free flow of trade between Great Britain and the region.

“We do think it’s very important the protocol does not place unnecessary barriers — or barriers of any kind — down the Irish Sea,” he said during prime minister’s questions.

His comments have raised pressure on Maros Sefcovic, European Commission vice-president, to agree to demands from London and Belfast to soften the need for checks on trade across the Irish Sea.

Mr Sefcovic held talks on Wednesday with Michael Gove, Cabinet Office minister; Arlene Foster, Northern Ireland first minister and leader of the Democratic Unionist party; and Sinn Féin’s Michelle O’Neill, deputy first minister.

In a joint statement issued late on Wednesday night after the virtual meeting, Mr Gove and Mr Sefcovic “condemned unreservedly any threats or intimidation”, in a reference to problems faced by port workers at Belfast and Larne who feared they were being targeted. Checks on food and agriculture products were suspended in both places for a second day on Wednesday.

After a “constructive discussion amongst all parties”, Mr Sefcovic and Mr Gove “concluded that the UK and the EU would immediately work intensively to find solutions to outstanding issues”, the joint statement said.

The pair have agreed to keep in close contact and meet again in London next week.

British officials had said the meeting was a chance for Mr Sefcovic to hear directly from Northern Ireland’s political leaders.

Ahead of the meeting Mr Gove wrote to Mr Sefcovic warning that the commission’s handling of the Northern Ireland issue in recent days had seriously raised tensions in the region.

Mr Gove said he wanted “grace periods” to allow the free flow of trade in certain goods across the Irish Sea to be extended until January 2023, pending permanent solutions. The extra time would cover supermarkets and their suppliers, chilled meat products, parcels and medicines.

With some of the grace periods due to expire on April 1, the extensions would allow businesses that regularly send goods from Great Britain to the region much more time to adjust to the arrangements, which came into force at the start of last month.

The Northern Ireland protocol was a key part of Mr Johnson’s Brexit deal. To avoid a hard border on the island of Ireland it left Northern Ireland under EU customs rules and part of the single market for goods.

But Mr Johnson’s insistence that the UK should leave the bloc’s customs union and single market meant that new checks were needed on goods moving from Great Britain to the region.

Mr Sefcovic is under considerable pressure after the commission last week briefly invoked the Article 16 override mechanism to allow Brussels to block the shipment of vaccines from the EU into Northern Ireland.

The threat of border controls on the island of Ireland infuriated both communities in Northern Ireland. Mr Gove told Mr Sefcovic in his letter “the reaction was even more negative than I expected”.

Nationalists bemoaned the fact that Brussels wanted to reimpose a border between Northern Ireland and the Republic, while pro-UK unionists urged Mr Johnson to use Article 16 to remove border checks for trade between Great Britain and Northern Ireland.

Both the EU and UK are entitled to invoke Article 16 in the event of the Northern Ireland protocol causing “economic, societal or environmental difficulties”.

The EU, which swiftly dropped its proposed use of the override clause late on Friday, had claimed there would be serious societal issues if the 27-member bloc did not have sufficient supplies of Covid-19 vaccines.

Mrs Foster has argued that the same societal problems were being stirred up by excessive bureaucracy on trade between Great Britain and Northern Ireland, leaving unionists feeling cut off from another part of their own country.

Mr Johnson and Mrs Foster met earlier on Wednesday. Downing Street said the prime minister promised to do “everything we could to ensure trade continues to flow effectively right across our United Kingdom”.

The DUP, which wants “permanent solutions developed” to lift barriers to trade, said the prime minister’s timetable for resolving the issues was the end of March. “Sticking plaster solutions and grace periods that kick the can down the road will not solve these problems.”

The Irish government, meanwhile, signalled it was open to “flexibility” in implementing the protocol and the extension of grace periods.

But Simon Coveney, Irish foreign minister, dismissed a fresh push by the DUP to scrap the protocol outright. “Those who are calling for doing away with the protocol entirely, I think, are completely unrealistic. That is not going to happen,” he said.

At a closed-door meeting of EU ambassadors in Brussels on Wednesday, Ireland’s envoy said the commission’s decision to trigger Article 16 without warning had caused damage in Northern Ireland that could not be easily “drawn a line under”, said people familiar with the matter. “It was a serious mistake,” said permanent representative Tom Hanney.

At the meeting, Mr Hanney asked the chief of staff to the commission’s president Ursula von der Leyen what Brussels would be doing to change its internal protocols to avoid such mistakes happening again, given that Dublin, London or Belfast were not notified of the measure.