Boris Johnson, the former prime minister, seen on his visit to Kyiv last month - Ukrainian Presidential Press Service/Handout via Reuters

Boris Johnson, the former prime minister, seen on his visit to Kyiv last month – Ukrainian Presidential Press Service/Handout via Reuters

Boris Johnson’s warning over Brexit is “not completely unhelpful”, Penny Mordaunt has said.

The former prime minister intervened on Saturday night to urge Rishi Sunak not to scrap the Northern Ireland Protocol Bill in favour of a new deal with the European Union.

The Bill allows the Government to tear up parts of the Protocol, including the powers of the European Court of Justice (ECJ) in Northern Ireland, although Mr Sunak is understood to consider the Bill unnecessary if he can strike a fresh agreement with Brussels.

In his first remarks on Brexit since leaving office, a source close to Mr Johnson said: “His general thinking is that it would be a great mistake to drop the Northern Ireland Protocol Bill.”

Asked on Sunday morning about the comments, Ms Mordaunt, the leader of the Commons, told Sky News: “Well, Boris is being Boris.

“But I wouldn’t say this is a completely unhelpful intervention. And I think as I say, the Prime Minister, I think, will acknowledge that having the Northern Ireland Protocol Bill there, having the work that the former prime minister did has helped us get where we are.

“But it’s always been our preference to try and have a negotiated settlement, and that is what everyone is working to [do].”

Penny Mordaunt - Kirsty Wigglesworth/AP PhotoPenny Mordaunt - Kirsty Wigglesworth/AP Photo

Penny Mordaunt – Kirsty Wigglesworth/AP Photo

Ms Mordaunt went on: “The intervention by a source close to the previous prime minister is helpful to remind the EU of that Bill, and what this deal actually has to do.”

A new deal is expected to be unveiled by Mr Sunak this week, but Northern Irish unionists in the DUP have warned the Prime Minister not to “cave in” over the Protocol Bill.

The legislation, which was voted through the Commons and tabled while Mr Johnson was still in power, is now in its report stage in the House of Lords.

On Saturday, London and Brussels issued a rare joint statement saying they had made “very good progress” on solving the Protocol issue.

While Ms Mordaunt may have played down the remarks by Mr Johnson, they will stoke fears of a growing rebellion among Tory MPs when a new agreement comes before Parliament.

Mr Sunak is facing pressure from within his own party to stand firm on the role of the ECJ, with several of the ‘Spartans’ who stood firm against Theresa May’s withdrawal agreement indicating they will vote against anything that continues to give Brussels a law-making role in Northern Ireland.

Many of the backbenchers who harbour concerns remained loyal to Mr Johnson until the end of his premiership, and some have expressed fears Mr Sunak will yield to European demands in a “betrayal” of what the former prime minister negotiated.

A senior Government official said: “If we can find a way to satisfactorily resolve the issues with the Protocol then you wouldn’t need the Bill. But we haven’t resolved them yet.”