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Fednav’s Umiak I. The Montreal-based company has ordered 12 new Great Lakes ships that will be equipped with chlorine and filtration systems, which ensure ballast water is cleaned before being released.

Ahead of controversial new shipping regulations, Canada's largest global shipowner said it is the first to fit its new vessels with filtration equipment designed to limit the spread of invasive species in the Great Lakes.

Montreal-based Fednav Ltd., which owns and operates 100 bulk freighters in the Great Lakes and around the world, said it has ordered 12 new Great Lakes ships that will be equipped with chlorine and filtration systems that ensure ballast water is cleaned before being released.

The company is taking the steps ahead of environmental regulations expected to go into force next year.

"We decided to go ahead with a system that we believe in, that we trust," said Marc Gagnon, director of government affairs at Fednav, which is owned by Montreal's Pathy family. "We want to be protective of the Great Lakes because it's a special market for us."

Ships that take on or release water used for stability are blamed for the arrival in the Great Lakes of such harmful species as zebra mussels and gobi fish in the late 1980s. In response, regulators of the Great Lakes and other important shipping routes have agreed to impose rules requiring ships to filter and clean the water.

The shippers that operate on the Great Lakes-St. Lawrence Seaway say the patchwork of rules on the way is confusing and expensive.

Canada's rules are expected to come into force in May, 2016, along with 29 other countries that have signed an agreement with the International Maritime Organization. The U.S., which shares operations of the Seaway with Canada, has not signed on. Instead, there are two sets of U.S. rules from separate federal agencies, the Coast Guard and the Environmental Protection Agency, on top of regulations from Wisconsin and Minnesota.

Adding to the confusion is Canadian ships docking in U.S. ports on the Great Lakes are subject to stricter rules than their U.S. counterparts, because their routes stretch farther east. Before spending millions of dollars fitting ships with filtration systems, companies say they need assurances they will meet regulatory approvals.

"It makes no sense from a business standpoint," said Robert Lewis-Manning, president of the Canadian Shipowners Association, which represents companies that operate 84 vessels on the Great Lakes.

Fednav said the first of the 12 filter-equipped ships, being built at Oshima shipyard in Japan, is expected to be delivered in the fall of 2015.

The company said it has spent millions of dollars over several years testing various filtration systems before settling on a Japanese-engineered system that works on fresh and salt water.

Mr. Gagnon said the systems cost less than the earlier multimillion-dollar estimates.

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