Its consultation on licensing regulations, published this week, calls for sales of alcohol to be made only in cordoned-off areas in larger shops or behind counters in smaller outlets.
Scotland's governing body says its aim is "to tackle antisocial behaviour, underage drinking, binge drinking, and problems associated with the misuse of alcohol".
But Fiona Moriarty, director of the Scottish Retail Consortium, said: "If the Executive thinks it can solve all of Scotland's problems with alcohol by where it sticks alcohol in a supermarket, it is wrong.
"We need to address the issue of alcohol misuse directly with those who are involved and not punish the majority of responsible retailers and consumers with restricted access."
There were also concerns that enforcement of restrictions would be determined by local licensing boards, she said. "This makes us very nervous, as restrictions could be determined not by a clear understanding of the issues among board members but simply by their own personal views on alcohol."
John Drummond, chief executive of the Scottish Grocers' Federation, said: "We have many members, such as the Spar group, who operate across several licensing borders and it would be inconceivable for them to have different regulations in different areas."
Smaller retailers had been caught up in a row that wasn't of their making, he claimed. "This is a proposal aimed at supermarkets' marketing of alcohol. There is a case for stores below, say, 3,000 sq ft being exempt from these new proposals," he said.
"We don't believe this is addressing alcohol misuse. Indeed it could be facilitating those who simply wish to buy alcohol and nothing else by enabling it to be served more quickly."
The deadline for responses to the consultation is 8 December.