Limiting the amount of water available for use by whisky distilleries could harm long-term plans, according to industry representatives.
Agreed in legislation passed at Holyrood, the limit prevents firms from taking more than 10 megalitres of water each day.
The Scotch Whisky Association said that, while no company uses anywhere near that limit, consideration should have been given to make the industry exempt.
Association chief executive Gavin Hewitt said: “We are disappointed that the Scottish Government did not include the Scotch whisky industry among the list of exempted activities when drafting the Bill, given its economic importance to Scotland. Even more unfortunately, we were not consulted on the issue.”
The concern was also raised by Conservatives, who called for assurances during the passage of the Water Resources Bill in Parliament.
Highlands and Islands MSP Mary Scanlon said: “The distilling process sees two-thirds of the water abstracted returned to source within two to 12 hours of removal.
“So, I would like the Scottish Government to consider the measurement being the water consumed rather than the water abstracted, which would overcome the concerns of the industry.”
Deputy First Minister Nicola Sturgeon pledged to discuss the issue with the whisky industry.