The federal government has had some troubles with the Supreme Court of Canada since taking office in 2006 (here is one recent example), but that's not the only court in Canada that has caused the federal government grief.

Several decisions of the Federal Court in relation to endangered species issues or other regulatory matters, like pest management, have highlighted serious deficiencies in decision making or actions from the federal government's ministers.

The most recent decision to suggest all is not well on the conservation front is related to the Minister of Fisheries and Oceans decision to allow the opening of a herring roe fishery on the west coast of Vancouver Island.

On February 20, 2014, Justice Mandamin of the Federal Court of Canada granted a request from five First Nations for an interlocutory injunction to stop the opening of the fishery. On February 28, 2014, the court issued its reasons.

This is an interim decision pending the hearing of the case on its merits, so it is possible that the Minister's decision will be upheld in the end, though not in time for this fishing season. For 2014, the fishery will remain closed, as it has been since 2006 for conservation reasons.

It is almost unheard of for a court to allow an interim injunction of this nature, but there were a number of reasons the court agreed with the Applicants to at least temporarily thwart the Minister's will, some unique to First Nation's constitutional rights and law.

To successfully obtain an injunction, the court considers three factors, as laid down by the Supreme Court of Canada: (1) is there is a serious issue to be tried; (2) if what is sought to be stopped goes ahead, will there be irreparable harm; and (3) who the balance of convenience favours, i.e. the Applicants or the Respondent Minister.

A serious issue to be tried

There was no dispute between the parties that a serious issue is to be tried. The court easily concluded there was because of the conservation issues and the Aboriginal rights of the Applicants to fish and sell fish in relation to the fish stock area.

Irreparable Harm

The court concluded that there would be irreparable harm because of the following:

(1) the Department of Fisheries and Oceans (DFO) bureaucracy recommended that the fishery should remain closed for 2014, a recommendation not accepted by the Minister;

(2) the concern on the part of the First Nations that the fishery had not adequately recovered, and the need to consider their views on conservation;

(3) perhaps most seriously, the court held "the setting of the total allowable catch at 10% instead of 20% as a precautionary approach" was, in the court's view, 'fudging the numbers', as it was not a science-based decision.  The court stated "it seems to me once the Minister and the DFO depart from science-based assessments the integrity of fisheries management system is harmed."

(4) the Applicants would lose their position and opportunity to reasonably participate in negotiations for the establishment of their constitutionally protected Aboriginal rights to a community-based commercial herring fishery.

Balance of Convenience

In this, the court  noted that it must consider the public interest; not just as between the Applicants and the Minister, or the Applicants and the commercial fishing sector, but also in reconciling constitutionally protected rights for the Aboriginal community. These rights require the Crown to act honourably, in accordance with its historical and future relationship with Aboriginal peoples.

Related to that, the public interest lies with giving recognition to Court declarations and directions, which require an honourable participation by the Crown in negotiations to resolve disputes. The court noted that to ignore or disregard such declarations not only ignores the obligation to follow court direction, but also lowers the standing of courts in the public eye.

The court concluded that while there would be an impact on the commercial fishery, that arose out of the Minister's decision to allow the fishery to open, and could be mitigated to a degree by reallocation of licences to different fishery locations.

The public interest also favoured upholding the DFO conservation approach. The court noted "this is not an instance where the Minister has chosen, with the support and advice of DFO and the assessment of of scientific evidence, to make a discretionary decision concerning the fishery."

Role of Science in Government Decision Making

Recent and ongoing commentary has noted that cuts to the federal government's environmental staff can be compared to the series of deep cuts that occurred in Ontario in the late 1990′s.  This did not have minor consequences in Ontario, leading as it did, at least in part, to the Walkerton Tragedy.

These cuts, as they appear designed to do along with other government decisions, will also mean a clear loss of an ability to make sound decisions based on science, which so heavily figured in the court's decision here.  Will it be harder to challenge decisions like these in the absence of scientific information before the court? It may well. Alternatively, the courts may also find that in keeping with the precautionary principle, no or poor information upon which to make decisions that require a scientific footing is as good a reason to interfere with ministerial decisions as clear information indicating reckless decisions.

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