Northern Ireland Secretary Brandon Lewis has insisted the new Bill is “lawful” and “correct” but Labour has accused the Government of “law-breaking”.
There is also likely to be some opposition from within Tory ranks, with a number of MPs believed to be unhappy with the legislation.
The Financial Times reported that an internal note had been circulating among those against the Bill, which said: “Breaking international law to rip up the Prime Minister’s own treaty is damaging to everything the UK and Conservatives stand for.”
The legislation will give ministers powers to override elements of the protocol, which was jointly agreed by the UK and EU as part of the Brexit Withdrawal Agreement to keep the Irish land border free-flowing.
The arrangements instead require regulatory checks and customs declarations on goods moving between Great Britain and Northern Ireland.
Unionists in Northern Ireland are vociferously opposed to the international treaty, claiming it has undermined the region’s place within the United Kingdom.
The DUP has blocked the formation of a new power-sharing government at Stormont following last month’s Assembly election in protest.
The Bill due to come before Parliament will see the Government move without the consent of the EU to change the terms of the protocol in a bid to reduce the checks on the movement of goods across the Irish Sea.
This could include allowing ministers to remove all customs processes for goods moving within the United Kingdom and enable the frictionless movement of agri-food goods staying within the UK.
It could also see businesses in Northern Ireland given the ability to choose whether to follow UK or EU regulations, depending on who they are trading with.
The EU has made clear that such steps would represent a breach of international law and could prompt retaliatory action from the bloc.
Mr Lewis has said he hopes the Bill will persuade the DUP to support the re-establishment of the Stormont institutions.
He has also said the Government will set out its legal position on the Bill when the legislation is introduced to Parliament on Monday.
Mr Lewis told Sky News on Sunday: “What we’re going to do is lawful and it is correct.
“We will be setting out our legal position on this. People will see that what we’re proposing resolves the key issues within the protocol that don’t work.”
But shadow chancellor Rachel Reeves said “it does look like the Government plans to break international law”.
She said: “This Government seems to be developing a record for law-breaking and it is not one that the Labour Party can support.”
While Mr Lewis committed to publishing the Government’s “legal position” on the matter, he insisted “governments don’t publish details behind advice given to ministers”.
Downing Street has said it will share only “a summary” of the legal advice it received with the public, which has led to accusations of a “cover-up”.
A No 10 spokesman said on Friday: “The Bill has been agreed by the relevant cabinet committees and will be introduced to Parliament on Monday.
“We will, alongside the Bill, publish a summary of the legal advice.”
Labour’s shadow Northern Ireland secretary Peter Kyle said it is “incumbent on ministers” to release the maximum possible legal advice, with “transparency about its origins”.
Liberal Democrat Northern Ireland spokesman Alistair Carmichael said the public deserves “full transparency” over the plan’s legal basis, warning he suspects a “cover-up”.
Asked why Downing Street was publishing only a summary of the legal advice, and not disclosing it in full, Mr Lewis told Times Radio: “Well, governments don’t publish details behind advice given to ministers, that’s part of … we have to have that free and open discussion as they’re formulating policy.
“But we are going to set out the Government’s legal position and our methodology for that.”