The Scotsman has learned UK ministers have been briefed that the proposal announced by the SNP on Monday breaks European competition laws.
And with at least two major trade organisations preparing legal challenges to minimum pricing, there is concern that the Scottish Government's actions might see UK government ministers dragged through the courts.
Civil servants have warned UK ministers that the Westminster government is responsible for maintaining European regulations and it would be held legally accountable, rather than the Scottish Government, if ministers in Holyrood pressed ahead with the proposal.
The Scottish Government is insisting it is "supremely confident" that its minimum pricing proposal is legally sound.
Scottish ministers argue they would be using existing laws and devolved government statutory instruments to impose minimum prices as a mandatory condition for a licence. And they still plan to have the proposal in place in time for Christmas.
But a senior Whitehall source told The Scotsman: "Basically we have been told minimum pricing is completely illegal.
"We are worried this will mean we will be taken to court as the responsible authority.
"The Scottish Government's proposal appears to be ill-thought-out and we don't even think it will work, because what is needed is a cultural change in Scotland and that is not going to be effected by making booze more expensive."
However, the source admitted there were currently no alternative ideas from Westminster on what to do about Scotland's alcohol problem.
The UK government's doubts were raised on the day the Scottish Tories and Lib Dems also came out against minimum pricing. They argued the policy would damage the Scottish whisky industry and also raised fears about the legality of the proposal. Labour MSPs remain divided on the issue and will not make their position public until after their conference.
Minimum pricing, probably 40p a unit, was the highlight of a package of proposals put forward by justice secretary Kenny MacAskill and health secretary Nicola Sturgeon on Monday.
The issue is seen as urgent because of the thousands of deaths and more than 45,000 hospital admissions each year for alcohol-related problems, which cost Scotland more than 2 billion.