The EU leaders said such a move would violate Britain's international treaty obligations under the Withdrawal Agreement signed by Mr Johnson and would lead to retaliatory measures.
In Northern Ireland, the power-sharing institutions are suspended, with the DUP refusing to join Sinn Fein in a new Executive or to allow the election of a speaker to the Assembly unless there is fundamental change to the protocol.
In the Belfast Telegraph, Mr Johnson said there was still a sensible landing spot where the interests of all sides are protected, including the integrity of the EU single market, which the protocol is designed to maintain.
He said that it would require a movement on the part of the EU.
He said that the EU has told us that it is impossible to make changes to the protocol text to solve these problems in negotiations, because there is no mandate to do so. He said We will always keep the door wide open to genuine dialogue. There is a sensible landing spot in which everyone's interests are protected.
The Government has a responsibility to make sure that the consumers, citizens and businesses of Northern Ireland are protected in the long term.
We will have a more detailed assessment and next steps to Parliament in the coming days, but ministers argue that change is necessary as the way it is operating is hurting businesses and hurting sectarian tensions, with Unionists feeling their position in the United Kingdom is being undermined.
Earlier in the day, Ireland's Foreign Minister Simon Coveney warned that there would be a consequence if the UK took unilateral action in breach of its obligations under international law.
He said that such a move would be deeply damaging to the UK-Ireland relations and would undermine the functioning of the institutions of the peace process in Northern Ireland.
The last thing the EU wants, the last thing Ireland wants, is the tension with the UK, particularly at the moment given what is happening in Ukraine, Russian aggression, and the need to work together on an international stage, he told Sky News's Sophy Ridge on Sunday.
It has been the briefings that came from the British Government this week that have raised a red flag in Dublin and in Brussels because the British government is now threatening to break international law to break a treaty they signed with the EU. Business Secretary Kwasi Kwarteng hit out at the BBC and Sky News in a round of broadcast interviews, saying it would take a very long time for the EU to implement new tariffs. It is up to the EU. If they went into a trade war, they think it would be completely self-defeating, but that is up to them, he said. Any tariff situation would have to go to arbitrators. It is not something they can do arbitrarily, and willy-nilly. Downing Street said on Monday that Johnson will use a series of private meetings in Belfast to deliver a tough message that any fix to the protocol must involve the parties coming together to form an Executive and Assembly. He is expected to say that while the UK Government will play its part in ensuring political stability, politicians must get back to work so they can deliver on bread and butter issues for the voters. Ahead of his visit, however, Sinn Fein, now the biggest party in the Assembly after the elections, accused the Prime Minister of being in cahoots with the DUP and supporting its blocking tactics.