More than 300 at-risk killer whales living in British Columbia waters year-round haven't been adequately protected by Ottawa, a federal court judge has ruled.

A judge ruled Tuesday the Department of Fisheries and Oceans has "acted unlawfully" by failing to implement sufficient measures to safeguard the whales' critical habitat.

"The government is the one who's supposed to be monitoring best practises towards the environment," said Stephanie Goodwin, B.C. director of Greenpeace.

"But what we're learning is without independent assessors or auditors or even independent watchdogs ... killer whales and their habitat aren't being protected, even though on paper the Canadian government says it is happening."

The lawsuit was brought by a coalition of nine environmental groups, including Greenpeace, the David Suzuki Foundation, Ecojustice, the Sierra Club and the International Fund for Animal Welfare.

They argued the DFO flouted laws outlined in the Species at Risk Act, which requires it to legally protect identified critical habitats of endangered and threatened species from destruction.

But instead, court heard the DFO tried to use policies and guidelines to accomplish legal protection and excluded protection for biological elements of the habitat. The groups said that amounted to an unlawful interpretation of the act.

Justice James Russell agreed, ruling the federal government failed to prevent significant threats to the habitat, such as toxic contamination and noise pollution. It also failed to protect the prey that whales depend upon, the declining wild salmon stocks.

Goodwin said it's now in the DFO's court to look to science and strike a committee that includes both scientists and experts from other fields.

"They need to come to common agreement around what are all the things we need to do, then figure out what are the legal and policy mechanisms to move this forward," she said.

Two populations of resident killer whales live off the B.C. coast, about 220 northern residents that are listed "threatened" and another 85 or so in the south that are listed "endangered."

Goodwin said even though it's now up to the government to take action, the only way to know if it complies is through monitoring.

"We can watch and gage their progress as an external monitoring force, and we can also let the public know that they should be watching for this," she said. "If the Canadian government doesn't take action on it, then they can let the government know with their vote."

A DFO spokeswoman said in an email the government is reviewing the court decision and determining its next steps.