The commission joined five EU member states in opposing the move, arguing it was in breach of European trade laws.
The Scottish Government now has until the end of the year to persuade the EC the measure is essential to improve health or face a lengthy and costly battle at the European Court.
Mr Neil – in his first statement on the policy since taking over from Nicola Sturgeon as health secretary – insisted he would fight to bring in the legal minimum price.
He said: "Minimum pricing will save lives and reduce the harm caused by alcohol misuse and I 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 their points, which we will.
"We are confident that we can demonstrate that minimum price is justified on the basis of public health and social grounds and I will continue to press the case for minimum pricing in the strongest possible terms.
"We will respond to the EC by the deadline of December 27."
Bulgaria, France, Italy, Portugal and Spain have all lodged objections. Like the EC's "detailed opinion" they have not been published but it is understood they claim that minimum pricing is in breach of laws protecting free trade across Europe.
Under the Scottish Government's plan to set a minimum price of 50p per unit of alcohol it will be illegal to sell a normal-strength bottle of wine for less than £4.69. The price of a standard bottle of Scotch would be at least £14 and vodka £13.13.
Countries where drinks can be produced cheaply have complained the measure would remove their competitive advantage.
MSPs passed legislation paving the way for the minimum price earlier this year despite a fierce rearguard action from the drinks industry, which warned of a possible legal challenge.
A spokesman at the EC's Industry and Entrepreneurship Directorate confirmed that, while it fully shared the aim of the legislation to tackle alcohol abuse, there was a "technical objection".
He said the measures in the legislation caused difficulties in terms of their compatibility with the EU Treaty and added: "We are in a process aimed at finding a solution to the legal problems."
In addition to the objections in Strasbourg, the Scotch Whisky Association trade body is pursuing an action through the Court of Session questioning the legality of minimum pricing.
Research from Sheffield University, commissioned by the Scottish Government, indicated that setting the minimum price at 50p would lead to 60 fewer deaths, 1600 fewer hospital admissions and 3500 fewer crimes in its first year.
After 10 years, there could be 300 fewer deaths annually, 6500 fewer hospital admissions and overall savings of £942 million.
Campbell Evans, of the Scotch Whisky Association, said: "We want to work with the Government to address alcohol abuse but minimum pricing is not the way to do it.
"We have seen an improving health picture in recent years and want to build on that."