The Scotch Whisky Association said any new tax would impact on the 10,000 direct jobs in Scotland and the 25,000 posts supported by the supply chain. The move would also damage communities that depend on the industry.
The tax proposal was raised by Professor John Kay, who served on the Scottish Government's Council of Economic Advisers.
He said a £1 tax levied on each bottle of Scotch whisky sold in Scotland would raise £1 billion.
Mr Kay said Scotland's national drink does not do enough for the country that gave it its name and firms based outwith Scotland were reaping the benefits.
However, Gavin Hewitt, Scotch Whisky Association chief executive, said: "It is a ludicrous suggestion that Scotch whisky, one of Scotland's few economic success stories, should be burdened with additional taxation.
"Any new tax would be passed on to consumers, which would reduce demand and stifle growth and new capital investment, much of it from foreign sources."
He added whisky exports generated £4.2bn for the UK balance of trade in 2011, earning £134 per second.
Islay councillor Robin Currie said: "We have to be careful we don't overtax whisky because it has a great market and we don't want to upset that."
Scottish Conservative finance spokesman Gavin Brown MSP said firms needed assistance.
But Scottish Green Party MSP Patrick Harvie said: "Slapping an additional tax on a bottle of whisky would raise useful funds."