The first freight arriving in NI under the new arrangements last month
But Simon Coveney said it should be improved where possible, rather than scrapped as unionists have demanded.
Unionists oppose that part of the Brexit deal, arguing it damages trade and threatens UK unity.
His comments come as the UK has asked the EU to agree to a long extension of grace periods for the Irish Sea border.
Currently, supermarkets and other businesses are being allowed to operate with reduced requirements for paperwork and certification when moving goods from Great Britain to the North of Ireland.
The first of those grace periods is due to expire in April, but in a letter to the EU the British government has asked for an extension until 2023.
NI’s First Minister Arlene Foster, who leads the Democratic Unionist Party, has announced plans to stop north-south activities related to the NI Protocol until action is taken to address what she called a “growing crisis” over the Irish Sea border.
But the deputy first minister, Sinn Féin’s Michelle O’Neill said the position adopted by the DUP was “reckless”.
Mrs Foster spoke to British Prime Minister Boris Johnson ahead of a meeting involving Ms O’Neill, Cabinet Office Minister Michael Gove and European Commission Vice-President Maros Sefcovic.
In a statement issued after the phone call, Mrs Foster said the DUP wanted to see “permanent solutions developed” to ease trade.
“Sticking plaster solutions and grace periods that kick the can down the road will not solve these problems.”
But the prime minister said he was committed to Northern Ireland and that the government would do “everything it needs to do” in order to ensure trade flows smoothly across the UK.
Speaking on Radio 4’s Today programme, Simon Coveney said the protocol needed to be “improved where possible within the parameters of the agreement” reached by the UK and EU in 2019.
“I recognise there are serious issues that need to be resolved and we need to work on that with the European Commission and with leaders in Northern Ireland,” he said.
“This isn’t going to be solved by cutting off relationships or throwing away the entire protocol without any credible alternatives as to what you replace it with.
“The protocol is only a month old and is part of an international agreement – we all have legal obligations in terms of its implementation, so the focus now needs to be on a calm discussion on how you make the protocol acceptable.”
SDLP leader and Foyle MP Colum Eastwood said it was “highly regrettable that the first minister had chosen to approach the challenges presented by Brexit in a way that will increase instability and heighten tension at a time of immense sensitivity”.
The Foyle MP again called for a moderation in language and for politicians to “dial down the rhetoric”.
Tags: