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The Northern Ireland secretary is to hold talks with political parties this week over the Stormont brake.
Chris Heaton Harris said the brake would act as a veto if European law was "going to affect Northern Ireland in a significant way".
It aims to give a future Northern Ireland Assembly a greater say on how EU laws apply to Northern Ireland.
He added that the Democratic Unionist Party (DUP) had asked for clarifications in several areas.
The DUP is boycotting Northern Ireland's devolved government at Stormont until its concerns about post-Brexit trading arrangements are addressed.
The Stormont brake is part of the Windsor Framework, signed to alter Brexit's Northern Ireland Protocol, and it was announced last week after months of talks.
It will mean goods moving from Great Britain which are staying in Northern Ireland would use a "green lane" at Northern Ireland ports, meaning they should face minimal paperwork and no routine physical checks.
Goods which are due to travel into the Republic of Ireland would use a "red lane", meaning they face customs processes and other checks.
The brake would allow the assembly to raise an objection to a new goods rule.
Mr Heaton-Harris was asked on Sophy Ridge On Sunday on Sky News if the Stormont brake was a delaying mechanism or veto.
"If it's going to affect Northern Ireland in a significant way we would veto EU law," he said.
"You can't be using a veto trivially but I don't actually think the Northern Ireland Assembly would be using that trivially".
'No renegotiation'
He said he thought that Northern Ireland businesses will still be able to participate in future UK trade deals.
"We are now left with with about 3% of what was existing EU laws are going to be in place after this gets adopted," he said.
"That is the bare minimum required to allow Northern Ireland businesses the access they have to the European single market at this point."
On Friday, the secretary of state said he would bring forward legal reassurances that Northern Ireland remains an integral part of the United Kingdom.
He also said the deal could not be re-negotiated.
More on new NI Brexit deal
Mr Heaton-Harris has previously said the Stormont Brake would likely operate like the current petition of concern in the NI Assembly.
Sinn Féin's vice president Michelle O'Neill said she cautiously welcomed the Windsor Framework and urged the DUP to return to the Stormont executive adding that "leadership" was needed from the party.
"They decided to walk away from the executive in order to influence the negotiation, but the negotiation is now complete," she told Sophy Ridge on Sunday.
"So, there's no reason for them to stay outside of the executive. They should be back round that executive table, taking on the matters of the day."
Ms O'Neill said she shared concerns with other political leaders about the Stormont brake.
"I certainly don't want any deal to replace a problem with a problem," she said.
"But these are things we can do whilst also being in the executive," she added.
Alliance leader Naomi Long said it was right that Stormont should have a say over the laws that operate in Northern Ireland.
"But the bar has to be high, Rishi Sunak said it has to be exceptional and it also has to be infrequently used," she told the Sunday Politics programme.
"If that's going to work, it's going to need to be defined clearly in legislation what the threshold is."
"And it needs to be able to stand up to judicial review," she added.
Speaking on Friday, DUP MP Gavin Robinson said it was important the party did not make a decision on whether to back the deal "by timescales".
Sinn Féin MP John Finucane has said the issues could be clarified "in parallel with a functioning assembly".
Social Democratic and Labour Party leader Colum Eastwood described the Stormont brake as "pointless".
Meanwhile, Ulster Unionist Party MLA Mike Nesbitt said: "If the DUP reject this proposal, or this framework, I really don't know what the next step is because you always need an alternative and I haven't heard anyone articulate an alternative".