The agency said the shortfall was $5.9-billion higher than in the first quarter and greater than analysts had expected.
The overall goods balance posted a $3.6-billion deficit in the second quarter, following three quarters of surpluses.
"Falling energy prices as well as production disruptions hampered resource sector exports, while rising imports dented the merchandise trade balance," wrote CIBC World Markets economist Emanuella Enenajor, who had predicted a $15.3-billion deficit.
This largely reflected trade with the United States, as the goods surplus with the U.S. narrowed by $5.5 billion to $9.9 billion, its lowest level since the fourth quarter of 2010.
Total exports of goods were down $3.6 billion, while imports expanded $2.3 billion in the second quarter.
"The acute worsening in the current account deficit — Canada’s broadest measure of trade to roughly 3.6 per cent of GDP in the second quarter — serves as a reminder that the currency’s strength is mainly due to capital (rather than trade-related) flows," she added.
The current account balance is the country's net income position covering merchandise trade, relative exchanges in services such as travel, and inflows and outflows of investments.
The second quarter showing leaves the Canadian dollar vulnerable if renewed global fears emerge, the economist said.
International sales of energy products fell by $4.5 billion, reflecting lower exports of crude petroleum to the United States on lower prices and volumes after record sales in the first quarter.
Industrial goods declined $500 million, mostly on lower volumes of metal ores, despite stronger exports of fertilizer and fertilizer materials. Machinery and equipment exports grew by $800 million, led by higher aircraft sales.
Automotive products exports were up $500 million, split between cars and automotive parts.
Higher imports were driven by automotive products, up $1.1 billion, with more than half coming from higher imports of automotive parts. Machinery and equipment imports were up $900 million while consumer goods increased by $600 million. Imports of energy products declined $800 million, mostly on lower prices.
The services deficit trimmed by $200 million to $6.2 billion on a $500-million increase in commercial services exports. This was partly offset by higher deficits for travel and transportation services on increased spending by Canadians on fares and travel expenses.
The investment income deficit increased by $200 million to $5.5 billion on lower interest on foreign investment.
Canadian banks earned lower interest on their foreign investments while payments on Canadian bonds and money market instruments held by non-residents were up. Profits earned by Canadians on their direct investment abroad declined but lower profits earned on foreign direct investment in Canada moderated the increase in the deficit.
Non-resident investors increased their holdings of Canadian securities by $28.4 billion in the second quarter, up from $6.1 billion in the first quarter amid declines in major global stock markets.
Foreign investors acquired $17.9 billion of Canadian bonds in the second quarter, on par with the quarterly average investment observed since the first quarter of 2009.