Chief executive John Beard said the move would lead to retailers delisting own-label Scotch, of which it is the leading supplier.
Jobs would be at risk at its Grangemouth bottling plant and a grain distillery near Inverness.
Beard said: “[A 50p level] would increase the price of own-label by 37.5% which has a huge impact on us and a lot of low-income families.
“There is enough precedence to suggest this is a very serious problem for Scotland.
“For Calais read Carlisle in the context of wine and stores on the Northern Ireland border.
“It’s a huge problem. It’s not about individuals driving to Carlisle – it’s about organised, crime, white van and illicit sales.
“Own-label would increase its price overnight to £14 [a bottle] where it would arguably be the same price as leading brands. Consumers given a choice would arguably choose the brand but the chances are the retailers probably wouldn’t even given them that option.
“From a consumer perspective, to have eight or nine products all priced at £14 is not choice.”