The EU will offer to remove a majority of post-Brexit checks on British goods entering Northern Ireland as it seeks to turn the page on the rancorous relationship with Boris Johnson.

Up to 50% of customs checks on goods would be lifted and more than half the checks on meat and plants entering Northern Ireland would be abandoned under the bold offer from Brussels.

The olive branch will be extended on Wednesday in defiance of the French government, which internally raised concerns about the proposed move by Maros Sefcovic, the EU’s Brexit commissioner.

It comes after David Frost, the UK’s Brexit minister, warned it would be a “historic misjudgment” if the EU did not consider scrapping and replacing the existing Northern Ireland protocol.

The offer from Brussels on Wednesday is designed to answer this, and the prime minister’s claim that 20% of all checks on the perimeter of the 27-member state EU bloc are conducted at the regulatory border between Northern Ireland and the rest of the UK.

In a further attempt to calm tensions, Sefcovic will say the proposals are not being tabled on a “take it or leave it” basis and emphasise that he recognises the protocol has not worked well enough.

A bone of contention remains between the two sides, however, in the form of a demand from Lord Frost that the European court of justice (ECJ) loses its role as the arbiter of EU law being applied in Northern Ireland.

Sefcovic has not included any proposal on the role of the EU court in his offer, and sources said there was shock in Brussels at how the issue had become an apparent UK red line in recent days.

In a speech on Tuesday in Lisbon, Frost said he believed the EU had been too hasty in dismissing the court’s role as a “side issue”. “The reality is the opposite,” he said. “The role of the ECJ and the EU institutions in Northern Ireland create a situation where there appears to be no discretion about how provisions in the protocol are implemented.

“The commission’s decision to launch infraction proceedings against us earlier this year at the very first sign of disagreement shows why these arrangements won’t work in practice.”

Frost, who was embroiled in a late-night Twitter spat with Ireland’s foreign minister Simon Coveney over his position on the ECJ earlier this week, added: “But it is not just about the court. It is about the system of which the court is the apex – the system which means the EU can make laws which apply in Northern Ireland without any kind of democratic scrutiny or discussion.

“Even now, as the EU considers possible solutions, there is an air of it saying: ‘We have decided what’s best for you, and will now implement it.’

“None of this, we can now see, will work as part of a durable settlement. Indeed without new arrangements in this area, no protocol will ever have the support across Northern Ireland it needs to survive.”

Frost also reiterated his threat to trigger article 16, effectively suspending parts of the protocol, if the EU fails to deliver.

“It is our responsibility to safeguard peace and prosperity in Northern Ireland, and that may include using article 16 if necessary,” he said. “We would not go down this road gratuitously or with any particular pleasure.”

Beyond lifting an EU prohibition on British sausages and garden plants, Sefcovic’s intention is to reduce all so-called sanitary and phytosanitary (SPS) checks to what is regarded in Brussels as an extremely low level.

The EU will also vastly reduce the level of customs paperwork by broadening the definition of what products from Britain will be regarded as “not at risk” of entering the wider single market from Northern Ireland.

The commission will also suggest ways in which Northern Ireland’s stakeholders can have a voice in EU decision-making in recognition of the democratic deficit.

Sefcovic is understood to have faced heavy resistance from within the EU power structures over his package. France, in particular, fresh from a bruising encounter with the UK over fishing licences, had warned of the risks to the single market posed by lifting controls.

But Sefcovic won the internal argument and will further signal to Frost that the proposals are not being tabled on a “take it or leave it” basis. He will instead publicly ask Frost to work with them to flesh out his ideas for a new bespoke arrangement.