Lord McConnell said the growing row over which powers currently held by the EU in devolved areas like agriculture and fisheries are devolved could otherwise end up at the Supreme Court.
The former Scottish Labour leader also warned that the detail involved in repatriating thousands of EU regulations meant Holyrood would need its own Great Repeal Bill to ensure legislation complies with Scots law.
“We have a really quite critical situation emerging as a result of the vote last year, and the government’s strategy,” Lord McConnell told a House of Lords committee. “I worry deeply that the polarisation of the two positions could lead to some real problems further down the line in Scotland.”
He said the UK government should respect the current devolution settlement when deciding on powers, and called for flexibility on Brexit terms for Scotland.
“I think everybody has to fully understand that if there are going to be special arrangements for Northern Ireland... then it is simply not true to say there will be one solution for the whole of the United Kingdom, and therefore there needs to be some flexibility in relation to Scotland, and Wales as well.”