The groups say the environment and fisheries ministers have delayed final recovery strategies for four critically endangered species well past mandatory deadlines set out in the Species At Risk Act.
The coalition wants the judge to declare the delays "unlawful" and order those recovery plans.
"We're not before you this morning to talk about a minor or technical breach of the statute. We're not here a week or two after the deadlines have passed," Sean Nixon, the lawyer for Ecojustice, told Justice Anne MacTavish.
"We're here four or six years, depending on the species, after the mandatory deadlines."
The court action filed by Ecojustice on behalf of the Wilderness Committee, Sierra Club, David Suzuki Foundation, Greenpeace and Wildsight, cites the Pacific humpback whale, the Nechako white sturgeon, the marbled murrelet and the southern mountain caribou.
At the time the lawsuit was filed in late 2012, the final recovery strategies for these four species were between four and six years overdue.
All four species named in the court action are affected by oil and gas expansion plans in British Columbia and Alberta, in particular the Northern Gateway pipeline proposal, the groups said.
Last fall, after the federal review panel weighing the Northern Gateway stopped hearing evidence, Fisheries Minister Gail Shea published a final recovery strategy for the Pacific humpback whale.
In December, the ministry published a draft recovery strategy for the Nechako white sturgeon and the draft plan for the murrelet was published on Tuesday, the eve of the hearing.
Brian McLaughlin, the lawyer for the federal government, told MacTavish on Wednesday that the environment minister commits to publishing a draft strategy for southern mountain caribou by Jan. 17.
Lawyers for the federal government will argue their case to the judge on Thursday.
In written submissions, government lawyers said Ottawa does not dispute that the timelines set out in the act are legally required to be met, but they argued that with the publication of the final and draft recovery plans there is no remaining dispute.
That's not good enough, Nixon said.
"It's not just the four species at issue here. It's the other 164 species that also await protection," he said.
The lengthy delay and widespread non-compliance with the Species At Risk Act, "calls for a strong response from the court," he told MacTavish.
"The longer you wait, the more they decline," he said.
It is the sixth court case brought by environmental groups against the federal ministers for failure to comply with the species at risk law.
A similar court case in Alberta over the sage grouse resulted in an emergency protection order issued last month. That order would restrict oil production in areas near the sage grouse's habitat as of Feb. 18 but the order is being challenged in court by the City of Medicine Hat and LGX Oil & Gas Inc.
Environmental groups won a Federal Court victory five years ago over the recovery strategy and habitat protection for the Nooksack dace, a critically endangered fish once plentiful in streams in southern B.C. and Washington state.
"We find ourselves having to continue to go back to court to force the government to follow some fairly clear language in the act," Devon Page, of Ecojustice, said outside the court.
The recovery strategy for the Pacific humpback and the other draft plans came too late for consideration by the federal panel that decided last month the Northern Gateway could go ahead, said Caitlyn Vernon of the Sierra Club of B.C.
"That science should have been under consideration by the regulators, the public and the politicians," she said outside court.
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