Suella Braverman, the Government’s chief legal adviser, did not deny reports she has approved the scrapping of large parts of the deal with emergency legislation.
European leaders have warned the UK not to make the incendiary move, amid fears it could provoke a trade war with Britain’s largest trading partner.
Ministers have been increasingly hinting they could take unilateral action, with Boris Johnson arguing the Good Friday Agreement is more important than the protocol he signed up to.
The Prime Minister said a new executive in Northern Ireland could not be formed under the rules set out in the 1998 peace agreement without changes to the protocol.
The Democratic Unionist Party is refusing to enter a powersharing administration without significant changes to the protocol designed to prevent a hard border with the Republic.
The DUP opposition comes as Sinn Fein for the first time became the largest party in Stormont after last week’s elections.
Ms Braverman did not deny the Times’ report that she believes overriding the protocol would be legal because the EU’s implementation of it is “disproportionate and unreasonable”.
She told BBC’s Question Time she could not comment because of conventions binding the Government’s law officers, but suggested unilateral action could be required.
“The economy of Northern Ireland is worth less than 1% of the whole EU economy, but yet the number of checks that they are applying on the Irish Sea is totally out of proportion to that, and is disproportionately bigger than the number of checks they apply on the rest of their borders,” she said.
“It doesn’t make sense, and therefore, I think it’s only right that we do take action.
“If this does actually go forward – because there’s a decision yet to be made, I have to be clear, and that is a decision for Government, Cabinet.
“But looking at the way things are at the moment, taking action to protect Northern Ireland and the integrity of the United Kingdom, taking action to remove the burdensome checks and bureaucracy on the border, which is causing traders to stop trading with Great Britain and in fact, move their trade to Northern Ireland.
“Taking action to try and re-establish the place of the Good Friday Agreement so that both communities feel part of Northern Ireland and the east-west connections are preserved just as strongly as north-south… that action is becoming painfully, apparently necessary.”
Sir Jonathan Jones QC, who resigned as the head of the Government Legal Department in 2020 over a previous attempt to override the protocol, warned the move could break international law.
He told BBC Radio 4’s PM programme: “If that’s been proposed now then that’s seriously problematic, and it feels like a rerun of what happened two years ago when the Government was proposing to break international law.
“We know that the EU will be very cross if that happens and I think it’s understandable that they would be cross, because this would be a unilateral act and it would very severely damage the relationship we will continue to need with the EU post-Brexit.”
Meanwhile, Lord Frost, the architect of the 2019 withdrawal agreement that included the protocol, was pressing for Mr Johnson to tear up the deal on Northern Ireland despite the risks of a trade war with the EU.
He used his Daily Telegraph column to say ministers have “no option now other than to act unilaterally to disapply part or all of the protocol”.
“We may, of course, face EU retaliation, though it would be disproportionate to the trade involved, only arguably legal and entirely self-defeating,” he wrote.