Whale advocates are troubled to discover that a Canadian Navy frigate was using sonar off San Juan Island in an area popular with endangered killer whales.

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Jeanne Hyde awoke before dawn on Monday to an odd, unnatural pulse coming from her computer.

The San Juan Island resident, a whale advocate, helps monitor an underwater network of audio-tracking hydrophones by sleeping next to a pair of speakers. She was groggy at first, but quickly leapt out of bed, hit “record” on her computer, checked a vessel-tracking system and called the Coast Guard.

“I knew it wasn’t a whale, and I knew it wasn’t right,” Hyde said Wednesday. “It took me a couple of seconds, but then I thought, ‘Oh my goodness, that’s sonar.’ “

After wrangling for years with the U.S. Navy over the use of mid-frequency sonar, environmentalists and whale advocates this week stumbled upon another noise source they fear could trouble endangered killer whales: the Canadian navy.

Between 5 a.m. and 6 a.m. that day, the Canadian frigate HMCS Ottawa employed sonar during a training exercise in Haro Strait just off San Juan Island — a popular route for killer whales and an area where the U.S. Navy avoids sonar without first getting permission from the National Marine Fisheries Service.

The frigate was in Canadian waters at the time, said Lt. Diane Larose of the Canadian navy. But the Ottawa’s sonar can travel 4,000 yards — more than two miles — and the sound was picked up by instruments in U.S. waters.

Larose said the Canadians are well aware of sonar’s potential to hurt killer whales, which communicate by sound at similar frequencies. In 2008, the Canadian Navy adopted a policy requiring the use of radar, passive acoustic systems, underwater listening devices and night-vision goggles to make sure marine mammals aren’t present when sonar is deployed.

“We take this very seriously,” Larose said. “It’s a very well-thought-out policy.”

But whale advocates said they tracked transient and endangered southern resident orcas near that area in the 24 hours before and after the ship sailed past, and said it’s always possible that a naval vessel might not see them.

“This was a fairly high-risk event as far as we can tell,” said Scott Veirs of Beam Reach, a marine-science school that helped establish the hydrophone network.

“In general, it’s concerning to me that the U.S. Navy has voluntarily refrained from unnecessary testing and training in the inland waters of Washington state, but the Canadian navy apparently still does,” he said. “The nightmare scenario is that you turn on sonar not knowing they are there and essentially deafen them either temporarily or permanently.”

Brian Gorman, spokesman for the National Marine Fisheries Service, said he didn’t know if his agency had been asked to look into Monday’s incident but said it is “responsible for protecting marine mammals everywhere they are in U.S. waters and we take that responsibility very seriously.”

The battle over sonar and its impact on whales has raged for at least a decade.

In May 2003, the U.S. Navy caused a stir when the USS Shoup conducted a training exercise in the same area. Several whale biologists saw what they believed were “abnormal” bunching responses by nearby killer whales. Sixteen porpoises were later stranded, suggesting to some that the animals’ hearing had been affected.

In follow-up investigations, the National Marine Fisheries Service could find no link to the porpoise deaths, but determined that the marine mammals almost certainly heard the sonar, though longterm hearing damage seemed unlikely. Navy biologists also disputed the claim that orcas had acted in any uncharacteristic way.

But the Navy has also acknowledged in several cases that midfrequency sonar has killed or injured several species of marine mammals.

This week, Veirs wrote about the latest incident on www.orcasound.net, a blog about the hydrophone network sponsored by The Whale Museum in Friday Harbor. The discovery also was picked up by a blogger for the Natural Resources Defense Council, an environmental group.

Lt. Larose, with the Canadian navy, said her country has taken into account all the scientific data about impacts to whales “and we’re trying to mitigate those measures as best we can.”

But “we also have to train our crews to know how to use this sonar,” she said.

Craig Welch: 206-464-2093 or cwelch@seattletimes.com. On Twitter @craigawelch.