The Protocol was agreed to deal with the problem of Northern Ireland having a land border with the EU and allow the rest of the UK to leave the single market to allow for trade deals, deregulation and VAT tax cuts.
But Mr Rees-Mogg insisted that it was always supposed to be temporary and reformed quickly.
“It’s fundamental really, the Northern Ireland protocol does not work,” he told MPs
The leading Brexiteer in the Government then lampooned demands that animals would need to be vaccinated for rabies from mainland UK to Northern Ireland.
“There has been no rabies in the UK since 1922 and we always used to be more concerned about rabies coming in from the continent,” he said.
The clearest way to get around the Protocol is to invoke Article 16 which means it no longer has any effect which Foreign Secretary Liz Truss has not ruled out in her talks with the EU.
Coming under questioning from South Dorset Conservative MP Richard Drax, he added: “We are one United Kingdom and it is important that that is maintained and the Protocol accepts that.
“Some of the details of the Protocol are simply not working and need reform.”
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Mr Drax said: “The Protocol is a major concern for many of us. The idea was to leave the EU lock stock and barrel. We haven’t achieved that yet until this Protocol has been resolved. How much longer are we going to put up with this?”
But Mr Rees-Mogg made it clear that his interpretation of deals with the EU are no longer legally binding.
He said: “Any commitments we now have are political-legal rather than legal-political. That is to say, they are agreements that have been made through diplomacy with political effect that may have a legal influence.
“Under the 1972 European Communities Act they were legal-political, that is to say, they were the law which required enormous political effort to change. So we have much greater flexibility.”
He also attacked EU officials and their Rejoiner allies in the UK who argue that Britain is stuck with the Protocol simply because it signed it.
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Mr Rees-Mogg noted: “There is a lot of commentary saying we signed it and therefore we should accept it lock stock and barrel, that’s absolute nonsense.
“We signed it on the basis that it would be reformed and there comes a point where we say ‘you haven’t reformed it therefore we are reforming it ourselves.’
“Preserving the United Kingdom is much more important than any agreement we have with any foreign power. That must be the case.”
He told MPs that he was limited in what he could say because Northern Ireland will shortly have elections for its devolved Assembly.
He said: “One has to be sensitive to the democratic process in Northern Ireland but what the Prime Minister says is accurate, what the Foreign Secretary has said is accurate. The wheels are in motion.”
He added that a “notwithstanding” clause within the deal meant the UK could change or ignore the Protocol without permission from the EU.
“We can do what we want ultimately,” he said.