The agency says sales in the motor vehicle and parts subsector dropped four per cent in what was a third straight monthly decline.
The second largest decline came in personal and household goods, where sales fell two per cent.
Sales in the machinery, equipment and supplies subsector decreased one per cent, the second decline in three months.
Wholesale sales were off in nine provinces, with the decrease concentrated in Ontario and Quebec, which have been on a downward trend since mid-2012.
Sales in Ontario fell 1.6 per cent in September partly because of declines in the motor vehicle industry, while Quebec sales dropped 1.7 per cent after rising slightly in August.