The Prime Minister said the post-Brexit trade treaty fails to command cross-community support in the region and is blocking the formation of a new government in the province.
It comes as US president Joe Biden waded into the ongoing row amid fears it could spark a trade war.
In a pointed attack, the White House demanded Mr Johnson show “leadership” by continuing negotiations with Brussels rather than tear up the deal to appease unionists.
“The best path forward is a pragmatic one that requires courage, co-operation and leadership,” a spokeswoman for the White House said.
“We urge the parties to continue engaging in dialogue to resolve differences and bring negotiations to a successful conclusion.”
European leaders have also warned the UK not to meddle with the Protocol.
German Chancellor Olaf Scholz stressed “no-one should unilaterally cancel, break or in any way attack the settlement”.
Irish Foreign Affairs Minister Simon Coveney said threats from the UK Government to override elements of the Protocol “have gone down really badly” with the EU.
Foreign Secretary Liz Truss is set to warn her EU counterpart today that Britain is prepared to take unilateral action to remove the Protocol.
She is expected to reiterate in a call with European Commission vice president Maros Sefcovic the risk to the Good Friday Agreement and warn that the situation cannot drag on.
Ms Truss has warned that some EU proposals are “a backwards step”.
At a press conference in Sweden, Mr Johnson faced questions over whether now is the right time to pick a fight with the EU against the backdrop of Russia’s invasion of Ukraine.
“The most important agreement is the 25-year-old Belfast Good Friday Agreement,” the Prime Minister said.
“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.
“Plainly the Northern Ireland Protocol fails to do that and we need to sort it out.”
Officials working for Ms Truss are drawing up draft legislation to unilaterally remove the need for checks on all goods being sent from Britain for use in Northern Ireland.
She is poised to take further action in the coming weeks if negotiations with the EU continue to stall.
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 that the protocol will not be completely overridden, with measures instead being considered to ease the issues on the ground in Northern Ireland.