A Government plan to override elements of Boris Johnson’s Brexit deal with Brussels would breach international law, a senior minister has confirmed.

The comment by Northern Ireland Secretary Brandon Lewis provoked a furious reaction, including from some Tory MPs, and followed news that the head of the Government Legal Department had resigned amid reports he was “very unhappy” with the proposal.

Mr Lewis told MPs legislation to ensure Northern Ireland could continue to enjoy unfettered access to markets in the rest of the UK would breach international law in a “very specific and limited way”.

In the Commons, former prime minister Theresa May warned the Government was in danger of losing the trust of other countries that it would honour its international agreements while Labour described the admission as “absolutely astonishing”.

Downing Street has sought to play down the changes in the Internal Market Bill – to be tabled on Wednesday – insisting they were simply “limited clarifications” to protect the peace process if they failed to secure a free trade deal with the EU.

But pressed in the Commons by the senior Tory MP Sir Bob Neill as to whether they were consistent with UK’s international legal obligations, Mr Lewis said: “Yes, this does break international law in a very specific and limited way.”

He said that the powers the Government was taking would enable ministers to “dis-apply” the EU legal concept of “direct effect” – which requires the enforcement of EU law – in “certain, very tightly defined circumstances”.

He added: “There are clear precedents for the UK and indeed other countries needing to consider their international obligations as circumstances change.”

However Sir Bob, who chairs the Commons Justice Committee, said adherence to to rule of law was “not negotiable”.

“Any breach, or potential breach, of the international legal obligations we have entered into is unacceptable, regardless of whether it’s in a ‘specific’ or ‘limited way’,” he tweeted.

Shadow foreign secretary Lisa Nandy said she was “astounded” by the minister’s comments.

“The rule of law keeps us safe, defends our national interest, and allows us to hold others to account. They are diminishing us on the world stage.”

Mrs May said ministers were now seeking to change the operation of an agreement which the Government had signed up to and Parliament had passed into UK law.

“Given that, how can the Government reassure future international partners that the UK can be trusted to abide by the legal obligations of the agreements it signs?” she demanded.

The row erupted as the pound plummeted against the US dollar amid fears that Mr Johnson’s chances of securing a post-Brexit free trade deal with the EU were diminishing.

It followed the shock announcement that the head of the Government Legal Department Sir Jonathan Jones had become the latest senior civil servant to quit his post.

No reason was given for his resignation but the Financial Times reported that he was “very unhappy” with the proposed changes to the Withdrawal Agreement.

The Prime Minister’s official spokesman said: “I can confirm that he is stepping down and we would thank him for his years of hard service and wish him well for the future.”

The news came as the EU’s chief negotiator Michel Barnier was arriving in London for the latest round of the negotiations on a free trade deal.

Ahead of his departure he said he would be seeking assurances from the UK that it was not seeking to backtrack on previous commitments.

In the Commons, Mr Lewis rejected suggestions that Britain would find it more difficult to negotiate trade deals with other countries as a result of its changes to the Withdrawal Agreement.

“There are some precedents in very specific technical circumstances in countries around the world, including some of those we will be looking to and are working to secure trade deals, to vary their position on international law as I outlined we will be doing in this situation,” he said.

However there were signs of unease among some Tory MPs that the UK was putting itself in breach of international law.

Sir Roger Gale said the UK was in danger of undermining its international credibility.

“Seeking to renegotiate the Northern Ireland protocol will be regarded worldwide as an act of bad faith,” he tweeted.

“Britain is an honourable country and that honour is not for sale or barter.”

Former minister George Freeman tweeted: “Oh dear. That sound you hear? It’s the sound of the Supreme Court preparing to remind ministers that intentionally breaking the law – even in a very specific and limited way – is, well, unlawful.”

The UK’s former ambassador to Washington Lord (Kim) Darroch told BBC Two’s Newsnight that the idea that the UK could “unilaterally rewrite” part of an international agreement is “unacceptable”.

Sir Jonathan’s resignation was followed by another at the Attorney General’s Office, with Rowena Collins Rice standing down as director general.

However, a spokeswoman at the department said the departure was “the result of a process dating back several months”.