Like-for-like sales for the month fell by 0.8%, when they had decreased by 0.8% in the corresponding month last year.
Total food sales were up by 2.3% in September 2012 while non-food sales increased by 1.4% on a year earlier when they had decreased by 1.2%.
‘Other non-food’ category was the month’s best performer for the first time since January 2011, partially fuelled by strong demand for tablets, games and gadgets.
In contrast, clothing and footwear category witnessed a less positive month.
The agency noted that September total sales growth was lower in Scotland than in the UK but the three-month averages remained very close.
In the three-month average, retail sales stood at 3.1% though September sales were marginally slow against recent months.
Considering shop price deflation at 0.2%, total sales in real terms were up 2%.
Scottish Retail Consortium director Fiona Moriarty said after a strong summer, these more subdued figures serve as a reminder that, while 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 on spending until Christmas gets closer," Moriarty added.
KPMG Retail head David McCorquodale said, "Having matched UK total sales for the past three months, Scotland’s figures fell behind this month."