The European Commission has produced a report warning it would be in breach of EU rules if it is implemented.
Scotland's new law will put a minimum price of 50p per unit on alcohol and is due to come into force next April.
Today, the UK Government will reveal plans for England and Wales to also set a minimum price, possibly at 45p.
But Catherine Day, European Commission general secretary, warned in the report the price increase would be "disproportionate and would create "market distortions".
The Scottish Government has consistently stated it is satisfied the law meets EU rules and is justified on public health grounds.
A similar battle is looming in England to that which the Scottish Government faced when it first revealed its plans for north of the border.
The British Medical Association and alcohol addiction campaigners are backing the minimum prices, while many in the drinks and retail industry are arguing against.
Scotland's minimum 50p price will mean a bottle of whisky will cost at least £14, while a bottle of wine will be £4.69.
But the European Union could overturn the legislation that has already been passed at Holyrood if it is deemed illegal under trade rules.
The EU has written with its concerns to the Scottish Government, which must respond before the end of this year.
Scottish Health Secretary Alex Neil said: "Minimum pricing will save lives and reduce the harm caused by alcohol misuse and we believe the policy, agreed by Parliament and backed by expert opinion, is the most effective pricing measure.
"The European Commission is in favour of addressing alcohol abuse and have asked us to consider its points, which we are doing.
"This is not unexpected and within the usual procedures for notification under the Technical Standards Directive.
"We are confident we can demonstrate minimum price is justified on the basis of public health and social grounds, and will continue to press the case for minimum pricing in the strongest possible terms.
"We will respond to the European Commission by the deadline of December 27."