The federal government's new budget bill sets out a controversial two-step approach to how industry should deal with fish and their habitat — with the second step much more far-reaching than the first.

It has taken environmental and industry lawyers a week to work their way through the complex fisheries provisions in the new omnibus budget bill.

They say the most puzzling thing is the inclusion of two different ways in which protection of fish habitat will change.

"This is just weird," said Andrew Gage, a staff lawyer with West Coast Environmental Law.

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A water-quality technician measures water quality near Fort McMurray, Alta. in 2011. The federal government's budget bill contains changes to the way fish habitats are protected in the face of major industrial projects. (Jeff McIntosh/Canadian Press)

One provision will come into effect as soon as the bill is passed. It maintains some protection of fish habitat, but it gives Ottawa more leeway to allow exceptions.

The second phase will come later — exactly when is unknown — and will allow industrial development as long as fish deemed important for commercial or aboriginal use or for a sports fishery aren't actually killed.

"This is the real new replacement," said Green Party Leader Elizabeth May, who has spent hours dissecting the measures.

For wildlife and the country's ecosystems, "it's devastating and sweeping," she said.

After hashing through the details with Fisheries officials, May believes the legislation will eventually eliminate protection of fish habitat, hand more oversight to provincial regulators and remove all federal impediments to natural resource extraction.

Regulatory changes in two stages

Why the rarely used, two-step approach? Because the government wanted to implement change soon, but needed extra time to develop a full-fledged set of regulations, officials say.

"Time will be required to develop supporting policies, procedures and regulations to implement this new prohibition," Fisheries spokesman Frank Stanek said in an email, adding that Ottawa will consult provinces, aboriginal groups, industry and conservation organizations.

He did not immediately answer questions about why the current regime could not be kept in place until the new one is ready.

In a teleconference April 24, federal Agriculture Minister Gerry Ritz said it could be months before all the changes are in place.   "(The changes) will require a piece of new legislation and this spring there will be consultation. The parliamentary committee system also allows for consultation."

The fisheries changes are woven throughout the budget implementation bill, and are so scattered that lawyers and experts are still scratching their heads even after a briefing from departmental officials.

The Assembly of First Nations, instead of responding directly to the changes in the Fisheries Act, published a list of 16 questions of its own about how the legislation will work.

The organization says it needs to know timelines, definitions of terms used in the legislation, plans for consultation and basic information about protection of aboriginal fishing rights.

The Mining Association of Canada would not comment on the bill until its lawyers thoroughly understand it.

Now, if companies want to mine or drill or run a pipeline, they must ensure they don't disrupt fish habitat and if they do, they must provide a new habitat for the fish.

Under the new provisions, habitat is not the main concern. They look at the fish themselves.

According to the wording in the budget bill, the government will only stop development if "serious harm" to fish is at stake, and only if those fish are part of a commercial, recreational or aboriginal fishery.

"Serious harm" is defined as death, or permanent damage to habitat.

As Gage points out, it does not include maiming, stunting or distorting the growth of fish. Proving a company has directly caused the death of important fish is very difficult, he added.

Federal ministers say they need the new rules because too much development is held up by legislation that protects ditches, puddles and minor streams.

They say the new provisions will also include stiffer penalties for companies that don't fall into line.

with a file from the CBC's Margo McDiarmid