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The US President has called on the prime minister to show “leadership” and press ahead with negotiations.
It comes amid reports ministers are planning to scrap of the agreement which has been a source of tension.
Now a White House spokesman has stressed the need for talks to continue to resolve the issues.
”The best path forward is a pragmatic one that requires courage, cooperation, and leadership. We urge the parties to continue engaging in dialogue to resolve differences and bring negotiations to a successful conclusion,” a White House spokesperson said.
White House officials and Northern Ireland minister Conor Burns are meeting in Washington this week.
Burns was sent to Washington in a bid to persuade Biden of the government’s strategy ahead of a formal announcement of its plan expected next week, according to the Times.
However, the newspaper reported the State Department felt “blindsided” after the plan was leaked.
Mr Biden, who has maintained close ties to Ireland, has repeatedly stressed the protocol is vital to protecting the Good Friday agreement.
It comes as ministers consider whether to introduce legislation overriding parts of the deal.
Officials working for foreign secretary Liz Truss are understood to be drawing up draft legislation to unilaterally remove the need for checks on all goods being sent from Britain for use in Northern Ireland.
Ms Truss, who is meeting with her European counterpart Maros Sefcovic on Thursday, is reportedly poised to take further action in the coming weeks if negotiations with the EU continue to stall.
During the meeting, she is expected to tell Mr Sefcovic that the UK will “not shy away” from taking action if the dispute over Northern Ireland drags on.
At a press conference in Sweden on Wednesday, Mr Johnson told reporters that the “most important agreement is the 25-year-old Belfast Good Friday Agreement”.
He added: “That is crucial for the stability of our country of the UK, of Northern Ireland. And it’s got to be that means that things have got to command across community support.”
But European leaders have strongly condemned the move.
German Chancellor Olaf Scholz has stressed “no-one should unilaterally cancel, break or in any way attack the settlement”.
The proposed law would allow businesses in Northern Ireland to disregard EU rules and regulations and remove the power of the European Court of Justice to rule on issues relating to the region.
Crucially, it would in parts override the protocol agreed by Mr Johnson in 2019 and mean the UK had breached its obligations under the Brexit agreement.
But it has been argued the protocol will not be completely overridden, with measures instead being considered to ease the issues on the ground in Northern Ireland.
Brussels is understood to be considering retaliatory measures if legislation reversing the protocol was pushed through, sparking fears of a trade war, The Times reported.