The main drag on the numbers was from the petroleum and coal product industry, which declined 9.6 percent to $6.4 billion due to seasonal plant shutdowns, the agency said.
Excluding that sector, overall manufacturing sales were up 1.2 percent.
"Sales fell in 13 of 21 industries, representing approximately two-thirds of manufacturing," StatsCan said. "Production in the aerospace product and parts industry rose 65.8 percent to $1.5 billion, following a 34.8 percent decrease in April."
There was continued good news in the motor vehicle manufacturing industry, where May sales were up 1.6 percent to $4.6 billion, its 10th increase in 11 months
"Sales in the motor vehicle industry were at their highest level since November 2007," the agency said.
Despite the sales decline, the agency said manufacturing employment has been growing since January, up 4.5 percent to 1.8 million people.