The UK has launched an audacious bid to rewrite a key plank of the Brexit deal, saying the Northern Ireland protocol was flawed at conception but served its purpose to get the UK out of the EU as “one country”.

The European Commission immediately ruled out a renegotiation of the deal, which was trumpeted by Boris Johnson as a solution to the Irish border impasse two years ago. The commission is understood to be open to some changes on the special arrangements for Northern Ireland, however.

EU officials expressed exasperation at the UK’s move, unveiled in a 28-page command paper by the Brexit minister, David Frost, on Wednesday. He told peers the protocol was unsustainable and said the UK “cannot go on as we are” given the “ongoing febrile political climate” in Northern Ireland.

With supermarkets warning they may pull out of the region unless there are changes, Lord Frost warned that the “burden” on shoppers and manufacturers would get worse without significant changes.

The proposals centre on four main issues, which would involve rewriting of articles 5 and 12 of the protocol:

*  Remove all customs checks on goods entering Northern Ireland from Great Britain but introduce a light-touch regime whereby businesses would register their trade and agree to inspections of their supply chains.

*  End the role of EU institutions in the enforcement of the protocol.

*  Introduce “a full dual regulatory regime” that would allow goods to circulate in Northern Ireland if they comply with either UK or EU standards.

*  Pass new legislation to introduce penalties for traders that do not comply.

The UK believes the changes would remove barriers to supermarkets, online shoppers and manufacturers, and secure the future of British supermarkets in Northern Ireland.

Frost stopped short of ripping up the document completely or triggering the article 16 provision, which enables either the UK or EU to suspend part of the arrangements in extreme circumstances.

However Maroš Šefčovič, the EU vice-president in charge of EU-UK relations, said Brussels has sought “flexible, practical solutions” and “will not agree to a renegotiation of the protocol”.

“The protocol on Ireland/Northern Ireland is the joint solution that the EU found with the prime minister, Boris Johnson, and Lord Frost – and was ratified by the UK parliament – to address the unique challenges that Brexit, and the type of Brexit chosen by the British government, poses for the island of Ireland,” he said.

Privately UK sources admit that the protocol, which was to break the three-year impasse over the Irish border, was flawed but did the job of getting the UK out of the bloc without leaving Northern Ireland behind.

This view appeared to be confirmed in a new excerpt from the BBC’s interview with the prime minister’s former aide Dominic Cummings, who said the protocol had been a “fudge”.

Both sides had wanted to “sign up to something that was not what either side really wanted and which punted difficult questions into the future to figure out later”, Cummings added. He reportedly told MPs in January last year to support the protocol because it could be changed later.

But business leaders in Northern Ireland urged negotiators to find a non-political, mutual solution to end the disruption and extra costs. “It is clear that the real-life experience of traders since 1 January needs to be understood, appreciated and inspire some honest and focused discussion, alongside business, to ensure that the workable and lasting processes are put in place,” said Stephen Kelly, chief executive of Manufacturing Northern Ireland.

Frost argued that EU relations would remain poisoned if a deal on the protocol was not done and urged Brussels to “return to a normal treaty framework similar to other international arrangements”.

“The difficulties we have in operating the Northern Ireland protocol are now the main obstacle to building a relationship with the EU,” he said. There was still time to do a fresh deal rather than triggering article 16, he said, adding: “We concluded that it is not the right moment to do so.”

Sources say the UK is committed to the protocol and thinks the right place for checks is the Irish sea, and briefed EU and US diplomats on Tuesday of their proposal to end the dispute.

Anton Spisak, a Brexit analyst at the Tony Blair Institute, said the UK move amounted to a “renegotiation of the withdrawal agreement” as it was “asking for changes to fundamental provisions of the protocol, especially article 12, that the joint committee [EU-UK joint governing body had] no powers to amend and modify”.

The shadow Northern Ireland secretary, Louise Haigh, said current instability in Northern Ireland had “destroyed trust in the UK government – an essential component of the Good Friday agreement”. Conservative MP Simon Hoare, the chair of the Northern Ireland affairs committee, said he feared the kind of trust needed to end the dispute was “in short supply”.

The UK hopes that if the EU agrees to pause further implementation of the protocol, space will be opened up for negotiations to get to the “heart” of the matter.

Businesses in Northern Ireland urged an agreed solution to be implemented as fast as possible, warning of severe consequences for the economy.

Aodhán Connolly, director of the Northern Ireland Retail Consortium, said any solution had to be mutual. “Without this, there can be no stability.”