Global chip supply disruptions are expected to bite again in May, the agency said, and economists predicted it could be many months before the situation stabilized.
Analysts polled by Reuters had predicted a deficit of C$700 million after a revised C$1.35 billion deficit in March.
Imports dropped 4.7% on a 22.1% plunge in shipments of motor vehicles and parts, as many manufacturers in North America and abroad stopped or slowed production.
Overall exports fell by 1.0% as shipments of motor vehicles and parts dove 18.1%.
"Production disruptions in the Canadian industry because of the shortage have been most significant in April. Production in May is expected to be slightly less severely impacted," Statscan said in a commentary.
The Canadian dollar slipped slightly to 1.2083 to the U.S. dollar, or 82.73 U.S. cents.
Ross Prusakowski, principal economist at Export Development Canada, said the problems could last till 2022.
"It's challenging. You've got the supply constraints, you've got the impacts of COVID-19 and you've got the global demand for goods, all of which now have semiconductors," he said by phone.
Exports to the United States, Canada's largest trading partner, rose by 1.4% in April, while imports fell by 5.2%. Canada's trade surplus with its southern neighbor jumped to C$6.40 billion from C$4.20 billion in March.
Stephen Brown, Canada economist at Capital Economics, predicted gross domestic product fell by 0.8% in April.
"Export demand is improving but, given the ongoing supply disruptions, we will have to wait until the second half of the year before exports start to rise strongly again," he said in a note to clients.
($1=1.2070 Canadian dollars)
(Reporting by David Ljunggren in Ottawa and Fergal Smith in Toronto; Editing by Andrew Heavens, Paul Simao and Jonathan Oatis)
By David Ljunggren
