The UK and Scottish Governments have clashed after Whitehall insisted it respected “the spirit and the letter of the devolution settlement" as it pressed ahead with Brexit without the consent of the devolved administrations.

The clash came as the Tory administration suffered a defeat in the House of Lords over the rights of EU citizens lawfully residing in the UK after Brexit.

Steve Barclay, the Brexit Secretary, in letters to Scottish and Welsh ministers addressing their refusal to give legislative consent to Boris Johnson's Brexit deal, said he recognised the "significant role" played by the legislative consent process.

He said despite the Sewel Convention - holding that the UK Government should "not normally" press ahead without legislative consent motions from devolved administrations - the circumstances of the UK's departure from the EU were "specific, singular and exceptional".

Earlier this month, MSPs at Holyrood voted by 92 votes to 29 to reject the Prime Minister's Withdrawal Agreement Bill[WAB] while Mark Drakeford, the Welsh First Minister, has urged assembly members to vote it down when it comes before the Senedd in Cardiff.

On Monday, members of the newly-restored Stormont Assembly in Belfast also rejected the Government’s Brexit deal after a near-three hour debate.

In a letter to Michael Russell, the Scottish Government’s Constitutional Relations Secretary, Mr Barclay made clear the UK Government would be ready to continue to engage with the Scottish Government as the WAB moved through its remaining stages at Westminster.

Expressing disappointment at Holyrood’s position and acknowledging the “distance” between the two governments’ positions, Mr Barclay nonetheless said: “I know we both recognise the enduring power and value of our historic relationship and also the important role of the legislative consent process; a principle to which the UK Government remains committed."

He told Mr Russell that through significant engagement on the legislation and the changes made to accommodate the Scottish Government’s concerns “we have at every stage respected the spirit and the letter of the devolution settlement".

The Secretary of State added while the UK Government would proceed with its legislation, despite not having Holyrood’s consent, it would "continue to work to address your concerns".

However, Mr Russell accused the UK Government of "ripping up the rules" and ignoring Scottish voters, MSPs and Scottish ministers to impose a hard Brexit.

Noting how all three devolved legislatures in the UK were poised to refuse consent to “this disastrous Brexit Bill,” he added: “If Boris Johnson presses ahead, it will demonstrate once again his contempt for devolution and the idea of the UK as a partnership of equals.”

In the Lords, peers backed a cross-party amendment to the WAB to ensure EU citizens had physical proof of their status.

It was the first defeat for the Conservative Government at the hands of peers since the General Election.

The vote, 270 to 229, a majority of 41, means the bill will have to go back to the Commons, where the Prime Minister will be able to use his 80-seat majority to overturn it.

Lord Oates for the Liberal Democrats warned that without physical documentation EU citizens, eligible to remain in the UK, would be "severely disadvantaged" in dealings with landlords, airlines, employers and other officials.

But Baroness Williams of Trafford, the Home Office Minister, warned the amendment could lead to "ID card creep".

She defended the digital provision of proof, insisting the service was robust and reliable, and warned physical documents could be lost, stolen or tampered with.

"The Government is adamant we must avoid the situation where years down the line EU citizens, who have built their lives here, find themselves struggling to prove their rights and entitlements in the UK," the minister insisted.