This is one where the existing wording is odd. There may be a subsequent amendment where the government is attempting to clean this up. As it's currently drafted, the minister will, “determine if the adverse effects within federal jurisdiction—and the adverse direct or incidental effects—that are indicated in the report are, in light of the factors...in the public interest”. I don't think any government would decide that an adverse effect was in the public interest. I think what they meant to say is what my amendment says; that where there are adverse effects—this is on a recommendation of the Canadian Environmental Law Association— “whether these effects are justified, in light of the factors referred to in section 63, because the project is in the public interest”.
I'd like to think that governments didn't decide that adverse effects were in the public interest. It's the project they're interested in, in whether the adverse effects are justified.