New Secretary of State Brandon Lewis has previously pledged that there will not be a border down the Irish Sea.
In a BBC interview in December, the then Security Minister disputed the accuracy of a leaked government document which warned that customs declarations checks would be highly disruptive and would separate Northern Ireland from Britain.
He acknowledged that some checks on goods leaving Britain for Northern Ireland would be required if those goods were then destined to leave the UK.
But he told interviewer Andrew Marr: "We are not going to have a border down the Irish Sea."
First Minister Arlene Foster and deputy First Minister Michelle O'Neill will meet the new Secretary of State this morning to discuss Brexit and the government promises made in New Decade, New Approach.
Mr Lewis replaces Julian Smith, who was sacked after just 204 days in the job.
Government sources last night dismissed claims that he was fired because of Downing Street's unease about legacy pledges in New Decade, New Approach.
They pointed instead to comments he made in the autumn on Britain's relationship with the EU which were interpreted as a put-down of Boris Johnson's powerful de facto chief-of-staff Dominic Cummings. Michelle O'Neill said she would be raising legacy issues with Mr Lewis at their meeting today.
"Reports from London that Julian Smith was sacked as a result of commitments made to bring forward legislation to implement the legacy bodies agreed at Stormont House are very concerning for victims of the conflict and their families," she said.
"The British government has already dragged this process out for more than five years, delaying the publication of legislation again and again.
"Some victims have been waiting up to five decades for truth and disclosure. It is unacceptable for the British government to backtrack on commitments made only weeks ago in the New Decade New Approach agreement.
"The British government must honour its agreements regardless of who is in the office of British Secretary of State."
Arlene Foster said she would raise the "key challenges" Mr Lewis is facing with him.
"We want to get Northern Ireland moving forward again. The Secretary of State has a key role in that process," she said.
"Mr Lewis will need to step up to the mark and show his commitment to the implementation of the New Decade New Approach deal and that he will be a positive voice for Northern Ireland at the cabinet table.
"Whether it is our hospitals or schools or infrastructure such as broadband, we need to work hand in glove with Her Majesty's Government to achieve the right outcomes."
SDLP leader Colum Eastwood said: "There are many challenges facing the Secretary of State and I hope he acts with fairness and integrity in dealing with the Executive at Stormont and on issues relating to the past."
Mr Eastwood said he looked forward to meeting Mr Lewis in the coming weeks.
UUP leader Steve Aiken said Mr Lewis faced a massive in-tray and couldn't let the grass grow under his feet.
He said: "I'll be asking the new Secretary of State to stand up for Northern Ireland and, even at this late stage, push back hard against the worst excesses of the Withdrawal Agreement which will impose a border in the Irish Sea. I hope that he'll show some mettle in cabinet and not be afraid to speak up against any further moves that undermine the integrity of the Union.
"It looks like we'll have an Irish government actively campaigning against the Union so it's long past time that our own Government got off the fence and started actively campaigning for the Union." TUV leader Jim Allister said that with Sinn Fein poised to enter government in the Republic, it was vital that the new Secretary of State adopted a "robust pro-Union position".
He said there must be a return to government policy that "Dublin has no say in the internal affairs of Northern Ireland".
Politicians from across the divide united to pay tribute to Julian Smith after Boris Johnson's reshuffle. Concerns were expressed about the effect on Stormont's fragile institutions.
Taoiseach Leo Varadkar hailed him as "one of Britain's finest politicians of our time".
Mr Varadkar said: "In eight months as Secretary of State, Julian you helped to restore powersharing in Stormont, secured an agreement with us to avoid a hard border, plus marriage equality. You are one of Britain's finest politicians of our time. Thank you."
Mrs Foster praised the outgoing Secretary of State for his "incredible" dedication. "Spoke with Julian Smith a short time ago to thank him for his help in getting devolution restored," she tweeted. "We may not have always agreed (we did sometimes) but his dedication to the role was incredible. Best wishes to him and his family. Always welcome in Fermanagh."
Mr Eastwood had harsh words for the Prime Minister, calling the sacking a "strategic error" by the Tory leader.
He said: "It defies belief that, after the successful restoration of power-sharing following a three-year collapse, Julian Smith's reward is a Cabinet Office P45."
Welcome to Northern Ireland, Brandon Lewis. In the last three-and-a-half years there have been five different Secretaries of State. During the Conservatives' near-decade in power the average length of tenure for the Northern Ireland Secretary has been less than 21 months.