If Mr. Patry wants to delete “intergovernmental”, I can't see why that's objectionable, on the face of it. I have no objection to what he is saying, unless someone can tell me where that would mean something different.
I'm just looking through the bill as it's presented. In clause 5, “agency” is not limited to intergovernmental. In subclause 4(2) it says “...the competent minister may consult with international agencies and Canadian non-governmental organizations.” Again, I don't see any harm in taking out the word “intergovernmental”.
Is that the point?