As a Nunavut court considered Thursday whether seismic tests in a proposed northern national marine park should be allowed, an official with the German institute behind the research expressed frustration with how Ottawa has handled the matter.
Heinrich Miller of the Alfred Wegener Institute said the Lancaster Sound project is caught in a quarrel between two Canadian government departments and his group is stuck in the middle.
"Somehow we got into this inner-Canadian controversy and are now being picked on as the bad guys," he said. "It is frustrating."
The institute's ship Polarstern is now sailing toward Lancaster Sound off the north coast of Baffin Island with permits to conduct seismic tests on the sea floor.
Dr. Miller says the tests concern distant geologic history and have no connection to looking for oil and gas deposits.
But Dr. Miller said that's not the message that has been relayed by the Canadian government, which is participating through the Canadian Geologic Survey.
"Someone in Canada came up with the idea that this was part of work looking for oil and gas in that particular region," said Dr. Miller, who spoke to The Canadian Press from a conference in Buenos Aires.
"We are aware of the interdepartmental controversy in Canada between the Environmental Ministry and the Ministry for Natural Resources.
"There was a probably not very conducive press statement issued by some of our Canadian colleagues which started off this whole controversy."
The idea that the government would search for energy resources while at the same time negotiating to turn the scenic and wildlife-rich waters into a marine conservation area infuriated local Inuit. So did the fact the tests were sprung on them with little consultation - which has also not escaped Dr. Miller's notice.
"We had relied on our Canadian colleagues to take care of that part," he said. "Apparently, this has failed."
As a result, lawyers for the Qikiqtani Inuit Association were in court Thursday applying for an injunction to stop the upcoming tests in Lancaster Sound.
They argued the government breached its constitutional duty to consult. They also said it failed to abide by conditions of the research permit granted by Nunavut's regulatory body that required scientists to take community concerns into account.
Federal officials, including Environment Minister Jim Prentice, have downplayed environmental risks and emphasized the government's commitment to protecting the sound.
But Dr. Miller wonders why it all came to this.
He points out that although the federal government has painted the Polarstern's cruise as part of routine resource assessment that goes on for every proposed park, it was his institute that approached the Geological Survey of Canada two years ago - well before the conservation area was announced.
"We are interested in how the present configuration of continental land masses in the North Atlantic and Baffin Bay evolved," he said. "We're still missing data from the structure of the Earth's crust, so it was felt it was good to have a cruise in the Baffin region."
That data would consist of relatively low-resolution information on the crust's deep layers. Energy explorers collect high-resolution data from shallower layers, Dr. Miller said.
"The type of data that we gather would not be looked upon favourably by the oil and gas industry. When you do pure scientific research, you may always come across by chance something that is a new find. But that's not what we are looking for and not what we are geared for."
Officials at Natural Resources Canada have consistently refused interview requests on the issue.
Dr. Miller said the Polarstern would be at work in Lancaster Sound for two days. The institute has worked in the Arctic and Antarctic for many years and is familiar with working around marine mammals.
The ship uses low-intensity seismic guns. Work will stop if any whale-watchers are spotted in the vicinity.
"Whatever we do, we respect the fragility of nature," he said. "The type of work we do, we do in a minimally invasive way.
"We are being ground up in this inner-Canadian controversy."