The Scottish Executive has pledged to protect and promote the drinks industry in Scotland.
Mr Wilson said whisky was one of Scotland's most important exports
Deputy Enterprise Minister Allan Wilson was speaking ahead of negotiations about the European Commission's proposed Spirit Drinks Regulation.
Mr Wilson said the new law, which would define whisky as a spirit produced using traditional methods, would safeguard the quality of Scotch Whisky.
However, he raised concerns about the proposed definition of vodka.
Britain is the EU's second-biggest vodka producer after Poland and Scotland accounts for about 80% of the UK's gin and vodka production.
Vodka can be made from many products, including cereals, sugar beet and cane sugar.
However, some European countries want to limit vodka production to alcohol made only from potatoes or cereal.
Mr Wilson said: "We want to see an inclusive definition of vodka which will protect current practices.
"We are confident there will be an amicable solution and are doing all we can, with our partners in the UK, to work towards this objective."
Mr Wilson said whisky generated millions each year for the Scottish economy and sustained thousands of jobs.
Nick Soper, European affairs director at the Scotch Whisky Association, welcomed the executive's support.
"The Spirit Drinks Regulation is of fundamental importance to Scotch Whisky distillers," he said.
"Adoption of the proposed definition of 'whisky' at EU level, which expresses traditional practice more clearly, will help to protect both consumers and Scotch Whisky in important export markets."
The proposed regulations would also include an explicit ban on the addition of other alcohol, sweetening or flavourings.