Because single malt whisky takes years to produce - by law, all Scotch whisky must be aged for at least three years - and the best are aged much longer - distilleries have been unable to quickly ramp up production.
About 20 million casks are currently maturing in warehouses in Scotland.
Experts say the shortage could last 10-15 years and push up prices considerably.
The Investment Grade Scotch Whisky Index, which tracks the value of high-end whiskies, increased by 14 per cent last year.
"We are currently working at full capacity - seven days a week, 24 hours a day," said Charlie Whitfield, a brand manager for Scotch whisky firm Macallan.
Macallan is currently building a 100 million ($210 million) second distillery which is expected to open in 2017.
American distillers making bourbon whisky are facing similar problems.