In a move that could spark a trade deal with Brussels, Ms Truss said the UK Government would bring forward changes unless an agreement could be reached.
It prompted an immediate backlash from the EU, Labour, and even some Tory backbenchers, who immediately sough clarity the Conservatives were still the party of law and order.
The move raises the prospect of renewed legal action against Britain by the EU, or even a trade war with tariffs placed on goods.
Other options could include ending trade and co-operation agreements, which would return Britain to a no-deal scenario, suspending things such as visa-free holidays and police co-operation, or even closing off access to EU waters.
To jeers from opposition MPs, Ms Truss insisted the changes were consistent with international law.
Making a statement in the Commons on Tuesday, Ms Truss claimed the Government remained “open” to a “negotiated solution”, but the “urgency” of the situation meant “we can’t afford to delay any longer”.
The foreign secretary said: “The Bill will contain an explicit power to give effect to a new revised protocol if we can reach an accommodation that meets our goal of protecting the Belfast Good Friday agreement.
“We remain open to a negotiated solution, but the urgency of the situation means we can’t afford to delay any longer. The UK has clear responsibilities as the sovereign government of Northern Ireland to ensure parity of esteem and the protection of economic rights.
“We are clear that the EU will not be negatively impacted in any way, just as we have ensured the protection of the EU single market since the existence of the protocol. We must restore the primacy of the Belfast Good Friday Agreement in all of its dimensions as the basis of the restoration of the executive.
“We will do so through technical measures designed to achieve the stated objectives of the protocol, tailored to the reality of Northern Ireland.”
Ms Truss pointed to the lack of functioning government in Northern Ireland, and said all sides knew changes were needed.
She said: “Regrettably, the Northern Ireland Executive has not been fully functioning since early February.
“This is because the Northern Ireland Protocol does not have the support necessary in one part of the community in Northern Ireland.
"I would also note that all of Northern Ireland’s political parties agree on the need for changes to the protocol.”
Ms Truss said the UK’s preference was to “reach a negotiated outcome” with the EU, but that Brussels’ proposals “would go backward from the situation we have today”.
She told the Commons: “Our proposed solution would meet both our and the EU’s original objectives for the protocol.
“It would address the frictions in east-west trade while protecting the EU’s single market and the Belfast Good Friday Agreement.
“The challenge is that this solution requires a change in the protocol itself as its current drafting prevents it from being implemented.
“But the EU’s mandate does not allow the protocol to be changed. That is why their current proposals are not able to address the fundamental concerns.
“In fact, it’s our assessment that they would go backward from the situation we have today with the standstill.
"This is not about scrapping the protocol. Our aim is to deliver on the protocol’s objectives.
“We will cement those provisions which are working in the protocol, including the common travel area, the single electricity market and north-south co-operation, whilst fixing those elements that aren’t, on the movement of goods, goods regulation, VAT, subsidy control, and governance.”
The Bill will propose separate “green” and “red” lanes for goods travelling between Great Britain and Northern Ireland, with those destined to stay within the UK freed from EU-level checks.
There will be no crossover between the channels, it is understood, with goods filtering through one or the other, depending on their intended destination.
The protocol was personally negotiated by Prime Minister Boris Johnson as part of the Withdrawal Agreement, but has seen constant criticism by ministers who have accused Brussels of abusing it.
They say the EU has insisted on overly stringent checks on goods travelling between Great Britain and Northern Ireland, which is causing trade disruption and community tensions.
European Commission vice-president Maros Sefcovic, who has been involved in negotiations, criticised the plan and warned Brussels could retaliate.
He said: “Should the UK decide to move ahead with a Bill disapplying constitutive elements of the protocol as announced today by the UK Government, the EU will need to respond with all measures at its disposal.
“Our overarching objective is to find joint solutions within the framework of the protocol. That is the way to ensure legal certainty and predictability for people and businesses in Northern Ireland.
“With political will and commitment, practical issues arising from the implementation of the protocol in Northern Ireland can be resolved.
“The European Commission stands ready to continue playing its part, as it has from the outset.”
Scottish Government constitution secretary Angus Robertson warned the plans could increase the likelihood of a recession.
He said: “Let us be very clear – to breach an international treaty, signed in good faith and hailed by the Prime Minister as a ‘fantastic’ moment, is bad enough.
“To contemplate this action when facing a cost-of-living crisis is unthinkable and indefensible.
“The Bank of England warns of UK recession this year and the UK Government provoking a possible trade war with EU could make it more likely."
Ireland’s foreign affairs minister Simon Coveney said the unilateral action from the UK was “damaging to trust”.
“At a time when people in Northern Ireland have chosen their elected representatives and want to get the executive back up and running, the path chosen by the British Government is of great concern,” he said.
But Mr Johnson insisted problems with the protocol must be addressed.
On a visit to Paddington station in west London, he said: “What that actually involves is getting rid of some relatively minor barriers to trade.
“I think there are good, common sense, pragmatic solutions. We need to work with our EU friends to achieve that.”
The controversial legislation is due in “coming weeks”, before the summer recess.
It had been heavily tipped to have been introduced to Parliament on Tuesday.
DUP leader Sir Jeffrey Donaldson said Tuesday’s move was “welcome, if overdue”, and a “significant” step towards getting power-sharing in Northern Ireland back up and running.
He told the Commons his party will take a “graduated and cautious approach” as the legislation progresses.
“We want to see the Irish Sea border removed and the Government honouring its commitment in the New Decade, New Approach agreement to protect Northern Ireland’s place in the UK internal market,” he said.
It is understood the UK would pull the Bill in the event of all of its aims and objectives being met by the EU.
The option of invoking Article 16 will remain on the table.