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Canadian Prime Minister Stephen Harper shakes hands with President of the European Commission Jose Manuel Barroso as they meet in Brussels on Friday, Oct. 18, 2013. Mr. Harper and Mr. Barroso will meet next week in Ottawa to sign a free-trade deal at a special ceremony.The Canadian Press

Canadian ship owners and their crews say Ottawa negotiated a lopsided trade deal with Europe that could eventually put thousands of jobs at risk.

Under the free-trade agreement, key pieces of the highly protected Great Lakes and the St. Lawrence River shipping business will be opened up to foreign competition for the first time, with no reciprocal access to the European market.

The complaints mark a rare pocket of domestic opposition to a deal that has enjoyed near-universal support among Canadian business groups.

Ship owners join dairy farmers in raising concerns about the agreement, which Prime Minister Stephen Harper and European Commission President Jose Manuel Barroso are due to initial at a special ceremony next week in Ottawa.

But unlike the dairy sector, where Canada stands to win unfettered access to the European market, the shipping concessions are one way.

The free-trade deal would allow European operators to carry empty containers in Canadian waters, bid on dredging projects as well as carry cargo between Halifax and Montreal.

"This will destabilize the industry and create a precedent," warned Martin Fournier, executive director of the St. Lawrence Shipoperators, which represents 14 companies who own more 130 ships. "The law was always quite strict about the protection of the Canadian industry."

Just as problematic for the industry is that Canada is opening up its market without getting matching access in Europe, Mr. Fournier pointed out. "We're opening our market to European ships, but the European market is closed," he said.

Robert Lewis-Manning, president of the Canadian Shipowners Association, worried that limited initial access for Europe could eventually morph into much broader competition down the road. "Our biggest concern has been the lack of information at this point," he said.

Roughly 44,000 people work in the Great Lakes and St. Lawrence marine shipping industry.

Under Canada's Coasting Trade Act, virtually all ships plying Canadian waters must be flagged in Canada, with crews trained and certified here.

Without those protections, the industry warned it could face unfair competition from lower-cost European operators. The Seafarers' International Union of Canada said ships flying European "flags of convenience" will be able enter Canadian waters "without any restrictions on origin of the crew, or level of wage and working conditions."

But Ottawa insists that the deal is overwhelmingly good for the country and the shipping industry. In a press release, the Department of Foreign Affairs and International Trade and Development said the Canadian shipping industry stands to gain from a projected increase in Canada-European trade.

The government also pointed out that the agreement would "ensure a level playing field for Canadian shipping companies" and that all existing safety, security and environmental regulations would apply to foreign vessels and their crews.

The government said it was merely responding to industry demands by agreeing to partly liberalize Canadian shipping laws.

The free-trade deal enjoys widespread support elsewhere in the marine industry, including among various port authorities and shippers. Ports have high hopes that the elimination of European tariffs on a range of agricultural products will dramatically boost volumes shipped through the Great Lakes and the St. Lawrence Seaway. According to the St. Lawrence Seaway Management Corp., the seaway system is currently operating at less than 50-per-cent capacity.