Britain is urging the EU to extend the Brexit "grace period" on trade between Northern Ireland and Great Britain to avoid more border chaos.
Cabinet office minister Michael Gove on Tuesday wrote to his counterpart in Brussels asking for the relaxation of checks and control to continue until 2023.
Boris Johnson's Brexit deal has already led to significant disruption between Northern Ireland and Great Britain, including shortages of some goods.
But the situation is expected to get worse in April unless the current grace period is extended.
Speaking on Wednesday morning Irish foreign minister Simon Coveney told public broadcaster RTE that his government thought the EU should show "flexibility" on the issue.
"From an Irish perspective we want there to be some flexibility here if it's possible to do that," he said.
Mr Gove is due to speak to EU vice president Maroš Šefčovič later on Wednesday to discuss the issue of extending the protocal.
He had told the Commons on Tuesday: "The end of grace periods for export health certificates and other issues do need to be addressed.
"I will be writing to Vice-President Maroš Šefčovič later today to outline some specific steps that we believe we need to take.
"Tomorrow, I will meet him and the First Minister and Deputy First Minister of the Northern Ireland Executive in order to ensure that we can make rapid progress through the Joint Committee."
The UK and EU have stood down some controls at Belfast and Larne ports following an “upsurge in sinister and menacing behaviour in recent weeks”.
Loyalists and unionists in Northern Ireland are unhappy at the new arrangements, which effectively put a trade border in the Irish Sea in order to keep the border with the Republic of Ireland open.
The Democratic Unionist Party has called on the government to suspend some of its obligations in the treaty under Article 16.
Boris Johnson on Wednesday morning spoke with Arlene Foster, the DUP leader and Northern Irish first minister.
A Downing Street spokesperson said the prime minister told Ms Foster "that we needed urgent action from the EU to resolve outstanding problems".
They added: "The Prime Minister restated his commitment to Northern Ireland as an integral part of our Union and underlined that we would do everything we could to ensure trade continues to flow effectively right across our United Kingdom."
In the House of Commons later, DUP MP Ian Paisley confronted the PM with his previous promise that businesses could throw any demands for paperwork on exports between Britain and Northern Ireland “in the bin”.
Mr Paisley said the people of Northern Ireland felt “betrayed” by the outcome of the Brexit deal and told Mr Johnson: “Prime minister, be the Unionist we need you to be.”
“The protocol has betrayed us and has made us feel like foreigners in our own country,” said Mr Paisley. “Tea and sympathy will not cut the mustard. What is the prime minister actually going to do?”
Mr Johnson responded that he was willing to override parts of the Northern Ireland protocol if necessary.
"We will do everything we need to do, whether legislatively or indeed by triggering Article 16 of the protocol, to ensure that there is no barrier down the Irish Sea," he said. However, the prime minister has agreed to a trade controls border down the Irish Sea.
So far, haulage firms have hiked prices by 12 per cent this week and hospitals, schools and prisons have warned of looming problems obtaining food supplies.
But the situation is expected to get worse when the grace periods on supermarkets’ paperwork and processed foods end, in April and July respectively.
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