The sound, which has also been described as a "hum" or a "beep", has apparently spooked the local wildlife in the Fury and Hecla Strait.
Paul Quassa, a member of the legislative assembly, said the noise was "emanating from the sea floor".
"That's one of the major hunting areas in the summer and winter ... And this time around, this summer, there were hardly any. And this became a suspicious thing."
The military said it was investigating what was causing the sound.
"The Department of National Defence has been informed of the strange noises emanating in the Fury and Hecla Strait area, and the Canadian Armed Forces are taking the appropriate steps to actively investigate the situation," an armed forces spokesperson told CBC News.