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Sockeye salmon make their way up the Adams River at Roderick Haig-Brown Provincial Park north of Chase B.C. October 12, 2010.John Lehmann/ The Globe and Mail

A structural reorganization of the Department of Fisheries and Oceans, meant to make the agency more efficient, led to confusion within government and a reduced ability to protect the environment, documents filed at the Cohen Commission indicate.

When DFO was restructured between 2004 and 2006, the department had to shift some key duties to Environment Canada - but not everything got picked up, the commission heard Tuesday.

One change called for DFO to hand over to Environment Canada responsibility for Section 36 of the Fisheries Act, which makes it illegal to deposit a deleterious substance in fish-bearing waters.

That regulation is one of the federal government's strongest laws when it comes to protecting fish habitat.

But Environment Canada already had a heavy workload and wasn't in a position to fully take over the job. The result was that support for Section 36 basically got lost in the shuffle, the Cohen Commission learned from documents filed as evidence.

An exchange of letters between Paul Macgillivray, DFO's regional director in the Pacific, and Don Fast, regional director for Environment Canada, showed how the two federal departments were struggling with the changes.

"Recently, DFO Pacific Region has lost considerable water quality expertise through attrition and program changes. The region is also facing severe financial pressures and is reducing its involvement in all regional programs. To this end, our S. 36 support role to EC is being reduced to a regional water quality co-ordinator function," wrote Mr. Macgillivray, in 2004.

Mr. Fast replied that the change would make it hard to protect the environment using Section 36.

"I recognize that your decision has been preceded by program changes and financial pressures in DFO Pacific Region," he wrote. "Nevertheless, it raises a number of questions about how Section 36 can continue to be effectively administered, given that EC does not have the capacity to fully absorb the water quality functions that DFO is withdrawing from."

He said the change would have "unavoidable implications" for the protection of fish habitat and water quality in the Pacific region.

Another document, a slide presentation for an internal DFO briefing, noted that the reorganization had led to the loss of the department's program to monitor toxins in the aquatic environment.

One slide stated the department's water quality unit had been "dismantled" and it said that raised "some uncertainty over who is the primary contact" on the issue.

Another slide suggested DFO's responsibility for testing for toxins in the aquatic environment, "really rests with 'some other agency,' " such as Environment Canada, the Canadian Food Inspection Agency, or Health Canada.

But the next bullet stated: "CFIA reminds us 'it is not our responsibility to manage your contaminated fisheries.' "

Also tabled with the Cohen Commission were minutes from an Environment Canada-DFO meeting in 2005, which showed that confusion over who was responsible for what had filtered down through the ranks.

"The message that some [Conservation and Protection]staff have rec'd is that they are no longer going to undertake Section 36(3) work. This is not DFO's position; however some [Fisheries Officers]have taken this approach due to the lack of clarity around DFO's Sec. 36 role and the lack of water quality support," stated the note.

The Cohen Commission was appointed by Prime Minister Stephen Harper to investigate the collapse of sockeye salmon populations in the Fraser River. It is currently holding evidentiary hearings in Federal Court in Vancouver.

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