Statistics Canada said Thursday that the deficit amounted to 3.4 billion Canadian dollars (2.5 billion US dollars), after two months of surplus.
In April, the country achieved a trade surplus of C$894 million.
Exports decreased by 3.8 percent, two-thirds of which were energy and agricultural and food products.
Exports of agricultural products and fishing recorded the largest decline in May, amounting to 13.4 percent.
The figures show that Canadian grain demand has slowed in recent months due to improved global supply, particularly for wheat and canola.
The energy sector, one of the main drivers of the Canadian economy, also saw exports drop by 7.3 percent in May due to falling prices.
In imports, most sectors saw a rise, with a total increase of 3 percent, or about C$2 billion.
Imports of unworked gold, silver, platinum and their alloys increased by 42.8 percent due to receiving large shipments of silver from the UK.
Statistics Canada attributes this rise to the state of economic uncertainty that leads to an increase in demand for precious metals.
Imports of automobiles and their spare parts rose by 4.5 percent.
The trade surplus with the United States, the country with which Canada conducts the bulk of its trade, narrowed to C$6.7 billion.
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