The glitches stem from bugs in software deployed last year centralising radio communications in the remote region.
"There are intermittent problems right now", Chad Stroud, president of the union that represents Coast Guard communications officers, told AFP.
"Somebody could be calling for routine traffic, or with distress, or an emergency like a 'mayday', and we may or may not hear the call."
As a result, the Canadian Coast Guard put out an advisory earlier this month alerting mariners to the situation.
Stroud said the matter could put maritime traffic "at risk", blaming the problems on budget cuts imposed by Prime Minister Stephen Harper's conservative government.
For several years now, Canada's Arctic waters have seen an uptick in traffic, especially through the Northwest Passage linking Asia and Europe.
"Because of global warming there isn't much ice up there and the traffic is increasing every year", Stroud said.
Harper's government has prioritised development of Canada's Arctic region, deciding to build a deep sea port there.
In contrast to Russia and the United States, Canada does not own a nuclear-powered icebreaker, limiting its reaction capabilities in the immense region.