The shortfall in June totaled C$1.13 billion ($1.06 billion) as the trade deficit ballooned from a revised C$695 million in May. The prior month was originally reported at a C$503 million deficit.
Exports dropped 2.5 percent in June to C$33.5 billion from C$34.4 billion in May, as exports of industrial goods and materials fell for a third straight month.
Imports at C$34.6 billion were exactly on expectations, reflecting a drop in energy products.
Canada's trade surplus with the United States narrowed to C$3.03 billion from C$3.45 billion. Meanwhile, the nation's deficit with countries other than the United States widened to C$4.16 billion from C$4.14 billion, the largest since December 2009.