All sectors reported sales decreases, bringing the national sum down by 1.4 percent to $48.8 billion from a month earlier.
"Sales in the motor vehicle and parts subsector were down for a third straight month, posting a 4 percent decline," the agency said. "This trend coincides with a decrease in imports of motor vehicles and parts during the same period."
Sales in the machinery, equipment and supplies sector also shrank, down by 1 percent.
The decline was seen in nine of the country's 10 provinces, concentrated in Ontario and Quebec, the agency said.
"Sales in Ontario fell 1.6 percent in September ... in part due to lower sales in the motor vehicle industry, which accounts for nearly 20 percent of the province's total wholesale sales," the report said.
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