BREXIT is having a profoundly destabilising effect on devolution but its implications have been largely overlooked in the UK-EU negotiations, according to a new report.

The document – The Brexit White Paper: What it Must Address – drawn up by academic think-thank the UK in a Changing Europe, says Brexit’s impact on Northern Ireland and the island of Ireland has been the most prominent issue in negotiations to date.

In a chapter on devolution, Edinburgh University Professor Nicola McEwen, who is associate director of the Centre on Constitutional Change, says that despite assurances from Prime Minister Theresa May, the preferences of the Scottish and Welsh governments have had little impact on the Whitehall’s negotiating position.

“Both devolved governments have argued strongly for the UK to remain within the EU internal market and the customs union,” she said. “They collaborated recently, ahead of the white paper, to urge the Prime Minister to pledge to stay in both.

“The Scottish Government, buoyed by a large majority of Scots voting Remain in the referendum and initially backed by cross-party agreement in the Scottish Parliament, had also argued that if the UK was to leave the internal market a way should be found to enable Scotland to remain within or closely aligned to it.

“This was formally rejected by the UK Government over a year later. However, if such a solution is agreed for Northern Ireland we can expect renewed demands from the Scottish Government for a differentiated solution for Scotland.”

McEwen said the devolved administrations would look to the white paper to provide greater detail on the nature of any future relationship with the EU, as they seek maximum regulatory alignment with the internal market and frictionless trade in goods.

She said they also wanted assurances on participation in EU programmes, including research and innovation funding, which has “benefited Scotland disproportionately”. The Welsh Government had also expressed concern about UK Government commitment to sustaining regional investment at levels Wales receives from the EU.

“The devolved governments have championed continued labour mobility for EU citizens and demanded assurances for EU citizens living in Scotland and Wales,” said McEwen.

“Scottish and Welsh ministers wrote jointly to the Home Secretary Sajid Javid in June to express concern about the lack of clarity over the EU Exit Settlement Scheme, and to seek a greater role in its implementation.

“The devolved governments have had a bigger voice within the domestic Brexit process, though they may dispute the extent to which that voice has been heard.

“Intensive intergovernmental discussions have focused on the EU (Withdrawal) Bill. Following unprecedented collaboration between the Welsh and Scottish governments, some concessions were secured which placed limits on the bill’s impact on devolution.

“These amendments, and the accompanying commitment from the UK Government to refrain from making legislative changes without seeking agreement from the devolved institutions, were sufficient to secure consent from the National Assembly for Wales. But they were insufficient to win the backing of the Scottish Government or the Scottish Parliament.

“That the bill was passed without the latter’s consent – the first time the Westminster Parliament has altered devolved competence in the face of opposition from the Scottish Parliament – has cast doubt over the future of the Sewel Convention, one of the founding principles of devolution.”

McEwen said that should the UK Government continue legislating in devolved areas without consent it could lead to further deterioration in Scottish-UK government relations.

“The Joint Ministerial Committee has already initiated an intergovernmental process to review whether existing structures are fit for purpose in a post-Brexit context,” she added.

“From a devolution perspective, new UK governance arrangements must provide space for a meaningful voice for the devolved governments and legislatures, including consenting powers in areas of devolved responsibility.

“Without this, further strains in the UK’s internal territorial relationships seem likely.”