The Scottish Retail Consortium (SRC), which reveals its latest survey today, said the figures highlight the fragile nature of the economic recovery. It hopes the "slight dip" will be reversed as retailers prepare to enter the crucial Christmas trading period.
The slowdown, which followed a 0.8% fall in like-for-like sales last September, means Scottish sales lagged the UK as a whole last month, with figures from the British Retail Consortium showing like-for-like sales had risen by 0.7% on September 2012.
Taking into account new store openings and shop expansion, total sales increased by 1.8% in Scotland in September, compared with 1% at the same time last year.
This compares with total sales growth of 2.4% for the UK as a whole in September, versus 3.4% last year, ending a three-month run of total sales in Scotland keeping up with those for the entire UK. However, the SRC said the three-month averages of Scotland and the UK remain close.
Taking shop price deflation of 0.2% into account, total sales in Scotland were up 2.0% in real terms.
SRC director Fiona Moriarty said: "After a strong summer, these more subdued figures serve as a reminder that, while some recent months have seen some shafts of light, the path to economic recovery remains fragile. While Scottish consumer confidence remained fairly stable in September, many of us are still cautious, and may be holding back spending until Christmas gets closer."
The SRC, which compiles its survey with KPMG, said food sales faded in September after a strong summer, with like-for-like sales down 1.3%.
Total food sales were measured at 2.3%, below an inflation rate of 2.9%, though the SRC noted strong demand for sandwiches and new launches in ready meals.
In non-food, total sales grew by 1.4% after falling by 1.2% a year earlier, but fell back by 0.3% on a like-for-like basis.
With warm temperatures continuing into September, and a lower than average rainfall, the SRC noted that total sales of clothing and footwear had declined as consumers delayed purchasing autumn and winter lines.
Women's clothing proved to be the best-performing segment, with sales of new seasonal styles beginning to filter through towards the end of the month.
On footwear, men's shoes performed best, with retailers pinpointing demand for casual styles. However, the later September holiday weekend, which pushed the Monday holiday into the October sales period, affected the children's segment in Glasgow and Ayrshire when compared with last year's figures.
Elsewhere, in non-food, September month saw strong demand for tablets, games and gadgets, making the 'other non-food category' the star performer for the first time since January 2011.
The SRC said the pick-up in demand for big ticket items continued, amid speculation the improving housing market had boosted sales of fitted kitchens. There was also said to have been a "revival" in sales of home accessories and DIY products.
In health and beauty, sales were "relatively soft", though premium cosmetics and vitamins were found to have sold well.
David McCorquodale, head of retail at KPMG, said: "Despite a setback, the forward momentum has been maintained in September and now the focus will be on the build-up to Christmas, with retailers determined to hold on to their margins as keenly as possible, while the ever-informed consumer holds out for a bargain.
"I look forward, with more confidence than trepidation, to a better Christmas on the high street."