He said the measures in the legislation caused difficulties in terms of their compatibility with the EU Treaty.
"We are in a process aimed at finding a solution to the legal problems," he said.
Earlier this month, it was revealed that Bulgaria has raised an objection to the legislation. It has now been joined by France, Italy, Portugal and Spain. The objections mean the consideration period for the proposals will be extended for a further three months to December 27.
The Scotch Whisky Association (SWA) lodged a complaint with the European Commission earlier in the summer, and is pursuing action through the Court of Session in Scotland.
A Scottish Government spokesman said: "We believe that minimum pricing will save lives and reduce the harm caused by alcohol misuse and we also believe minimum unit pricing is the most effective pricing measure. We are confident that we can demonstrate, under European law, that the minimum pricing of alcohol is justified in Scotland on the basis of public health and social grounds."