It was the first deficit in six months, although a revision took the previous month's surplus to a barely positive $152 million.
The agency says exports fell 1.2 per cent $39.1 billion in April, mostly as result of a 1.9 per cent decline in prices. In volume terms, exports fared better with 0.6 per cent increase
Meanwhile, imports edged up 0.1 per cent to $39.5 billion.
The biggest setbacks in exports came in shipments of industrial goods and materials, which fell 5.8 per cent to $9.3 billion. As well, shipments of machinery and equipment declined 3.1 per cent, with shipments of aircraft, engines and parts crashing 14.1 per cent.
Exports of energy products declined by 0.8 per cent to $9.9 billion, mostly due to a 6.7 per cent reduction in prices.
Partially offsetting the losses, automotive products rose 2.8 per cent to $5.5 billion in April, and agriculture and fishing products increased 3.8 per cent to $3.7 billion.
By countries, Statistics Canada says Canada's trade surplus with the United States decreased to $3.8 billion in April from $4.5 billion in March as exports declined 1.2 per cent and imports rose 1.3 per cent.
However, Canada's trade deficit with countries other than the U.S. narrowed to $4.2 billion from $4.4 billion in March, as exports decreased by 1.2 per cent and imports fell further by 1.9 per cent.