The Scottish Parliament is introducing new laws to control the licensing of shops to sell alcohol, which they say will combat Scotland's binge drinking culture.
Justice Secretary Kenny MacAskill said: "People have to recognise that selling alcohol is not a god given right - they choose to do it because they make a profit from it.
However tourist shops say it will be make it too expensive for them to sell whisky miniatures, and that the move could hit rural areas particularly hard.
The license will cost up to £1,800, and some of the shops involved claim that submitting layouts to architects in order to apply correctly for a licence will bring the total to £3,500.
Mary Scanlon, MSP for the Highlands & Islands said: "The small general grocer stores in the most remote and rural areas - for a one metre wide alcohol display they must pay £800 upfront to register, about £250 a year.
"They've also got to train their staff and get architects drawings in order to pass this. The whole thing is a bureaucratic nightmare."Miniatures are always part of any serious whisky collectors collection, but they can also be a way for a less wealthy collector to own a small amount of an extremely expensive whisky, where a full size bottle would be out of their price range.