Guto Bebb, Under Secretary of State at the Wales Office, commenting on a recent trip to Edinburgh, said he had left feeling "despondent" because it reminded him of the independent Irish Republic capital Dublin.
Scotland's first minister Nicola Sturgeon has announced that she will seek a second referendum on independence.
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And Mr Bebb, a Conservative party whip, who was in the Scottish capital for an British and Irish council meeting has said his "gut feeling" is that there has been a change in attitude in Scotland since the independence referendum of 2014 in which the majority voted to stay within the UK.
The meeting the Aberconwy MP was at brought together the devolved governments from Wales, Scotland and Northern Ireland, as well as the UK and Irish governments.
And writing in his North Wales Weekly News column, the former Plaid Cymru activist said that the First Minister's call for an independence referendum was "hardly a surprising development" as the Prime Minister comes closer to triggering Article 50 to begin the exit from the EU.
He said: "My brief visit to Edinburgh left me somewhat despondent because I felt the same way as I do when I leave Dublin.
"For me Dublin is somewhere which is recognisable but very different. That is fine in the context of the capital of an independent country but it should be a warning when visiting a city which is a crucial part of the UK.
"The sense of nationhood in Edinburgh is palpable. For a long time it has been satisfied within the UK.
"Even in 2014 a majority saw themselves as British and Scottish. Is that changing though? My gut feeling is yes and that should be a cause for regret to all of us."
The Welsh MP added: " "We have a huge amount in common with citizens of the Irish Republic, as we do Scotland," including similar television programmes, popular music and "in many ways a shared literature".
But he said "read their papers, listen to talk shows and watch the news and it's clearly another country".
Secretary of State for Wales, Alun Cairns was challenged about his minister's comments on ITV's Peston on Sunday Programme.
He described them as "speculation in order to develop the debate so that everyone in every part of the UK recognizes that we achieve more together".