Ms Truss said a law would be introduced to amend parts of the deal on how goods enter Northern Ireland from the UK.
Boris Johnson’s government agreed the deal with the European Union in 2019 after the Brexit vote.
But a row over its impact on trade has created a block on forming a devolved government in Northern Ireland.
In Parliament on Tuesday, Ms Truss said the proposed legislation would make some changes to the deal rather than scrapping it to resolve “the grave situation in Northern Ireland”.
In response to Ms Truss’s statement, the EU said it would “need to respond with all measures at its disposal” if the UK went ahead with the legislation.
Labour said the government should abide by the deal it signed and work with the EU “to find practical solutions to these problems” rather than altering the deal unilaterally.
The deal – known as the protocol – is a special arrangement that keeps the North of Ireland aligned with the EU single market for goods, avoiding a hard border with the Republic.
The arrangement ensured free trade could continue across the Irish land border, which is a sensitive issue because of the history of conflict in the North of Ireland.
But the protocol brought in some new checks on goods moving between Great Britain and the North of Ireland and has been criticised by unionist politicians since its introduction in 2021.
The DUP has refused to join the Stormont power-sharing administration until their objections to the protocol are dealt with.
On Tuesday, Ms Truss told MPs there was a “necessity to act to ensure institutions can be restored as soon as possible”.
She said the UK’s preference remained a negotiated solution with the EU in consultation with its negotiator Maros Sefcovic, who has been invited to London for more talks.
If a resolution cannot be reached, the UK would take steps to “cement provisions” that are working in the protocol, whilst “fixing those elements that aren’t”.
“The government is clear that proceeding with our legislation is consistent with our obligations under international law,” she said.
Elections to the North’s Assembly on May 5 resulted in a majority for politicians who accept the protocol, including the new largest party, Sinn Féin.
But the DUP has refused to join Stormont power-sharing administration until their objections to the protocol are dealt with.
Sinn Féin said the UK government was letting the DUP “hold society to ransom” after Mr Johnson met all political parties in Northern Ireland on Monday.
In a statement on Tuesday, Mr Sefcovic said the European Commission “stands ready to continue discussions with the UK government to identify joint solutions within the framework of the protocol”.
“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,” Mr Sefcovic added.
“Our overarching objective is to find joint solutions within the framework of the Protocol.”
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