The association says sales were down in about 60% of all local housing markets last month.
CREA president Beth Crosbie says affordably priced single family homes are in short supply in some of the hottest markets and that contributed to the monthly decline.
The number of newly listed homes fell by 1.6% in September compared with August.
Compared with a year ago sales were up 10.6%, while the average price for a home sold last month was $408,795, up 5.9% compared with a year ago.
However, excluding the Greater Vancouver and Greater Toronto markets, the average price was $325,406, up 4.5% from September 2013.
“Overall, the headline sales decline is a disappointment, although more data points will be needed to confirm a clear softening trend,” says Nick Exarhos of CIBC WM Economics in a note to analysts.