The UK wants to rewrite the Brexit deal on Northern Ireland amid a bitter standoff with the EU.
Britain said the protocol was disrupting trade and causing tensions in Northern Ireland which called the 1998 peace agreement into question.
David Frost, a minister overseeing post-Brexit arrangements, told Parliament that the protocol needed a major overhaul as he announced the UK would seek new negotiations with Brussels.
“There is a growing sense in Northern Ireland that we have not found the right balance, seen in an ongoing febrile political climate, protests and regrettable instances of occasional disorder,” he said.
“We have worked with the EU to try to address these challenges. But overall those discussions have not got to the heart of the problem. Put simply, we cannot go on as we are.”
Responding to Britain's announcement, the EU said it was willing to be flexible but that the protocol drawn up in 2019 must be implemented.
"We are ready to continue to seek creative solutions," said European Commission Vice President Maros Sefcovic. "However, we will not agree to a renegotiation of the protocol."
The pact was designed to avoid checks on the Irish border by patrolling goods before they enter Northern Ireland from mainland Britain.
London has angered Brussels by delaying these checks, describing the EU's demands as excessive. The EU says Britain knew what it was signing up for when it agreed to the deal.
In a foreword to a government paper on the subject, UK Prime Minister Johnson said the EU was being inflexible about the protocol and said the tensions “served as a drag” on post-Brexit ties with the bloc.
Anger over the protocol in Northern Ireland contributed to a week of unrest in April and the downfall of former first minister Arlene Foster.
Her eventual successor as Democratic Unionist Party leader, Jeffrey Donaldson, welcomed Tuesday's call to rewrite the protocol as a "significant first step" which showed that the arrangement is "not sustainable".
Trade disruption has led to cases of empty supermarket shelves, and the chairman of retailer Marks and Spencer said in a letter to Mr Frost that he could no longer ship many products across the Irish Sea.
What is the Northern Ireland protocol?
Brexit means that the border between Northern Ireland and the Republic of Ireland is now an external frontier of the EU.
Negotiators on all sides agreed that customs checks should not take place along this border, because of the risk of sectarian tensions.
Instead, the protocol provides for goods to be checked at an earlier stage – namely, when they cross from mainland Britain into Northern Ireland.
However, this arrangement has angered unionists who say it is weakening the link between Northern Ireland and the rest of the UK.
It has also led to concerns of trade disruption and empty supermarket shelves in Northern Ireland.
Britain, which says the EU is applying the protocol in an overly strict way, is now calling for the deal to be rewritten to address these problems.
Mr Frost said the UK would not use a provision known as Article 16 to suspend the protocol, but would call for a standstill in trading arrangements while diplomats seek a new deal.
“These proposals will require significant change to the Northern Ireland Protocol. We do not shy away from that,” he said.
He said new data-sharing arrangements with the EU and penalties for traders who break the rules could help to address the problems with the deal.
The EU says Mr Johnson’s government knew full well that there would be checks when it signed the Brexit deal.
“Britain decided itself to leave the single market of the European Union, to apply trade rules, to apply red tape to its goods that are leaving Britain, to goods that are coming into Britain,” Mr Byrne said.
The spat is being closely watched by Washington, where President Joe Biden has called for the 1998 agreement to be respected.