The research by scientists at Duke University in North Carolina tracked the decrease of sea ice due to global warming and the mortality of harp seals from 1992 to 2010.
David Johnston, a marine scientist who co-wrote the report, said it's the first study to show that seasonal ice cover in the four seal breeding areas of North America has receded by as much as six per cent per decade.
"There has been a string of light ice years recently and we're starting to be concerned that if ice continues to decline, this might have longer-term effects on the harp seal population," Johnston said from his office in Beaufort, N.C.
"I'm concerned that these animals are in for a tough road with what we're seeing with climate change."
The authors warned that they could see the disappearance of a year's entire seal pup herd due to a lack of ice, where females traditionally go to give birth every February and March. Pups usually drown if born in the water or on thin, unstable ice.
The study was funded by the International Fund for Animal Welfare, which has lobbied against the annual Canadian seal hunt. Johnston said the participation of the animal-rights group didn't affect the objectivity of the report, which was peer-reviewed.
He said researchers compared seal mortality rates to satellite images of sea ice in the Gulf of St. Lawrence, a critical area for seal breeding.
They also looked at the North Atlantic Oscillation, a weather phenomenon that affects the strength of winter storms and the formation of sea ice.
The research, published Wednesday in the science journal PLoS ONE, linked high seal death rates to a weaker North Atlantic Oscillation, or NAO, and the resultant poor ice conditions.
They found in 1969 the NAO was weak and the ice cover in the Gulf of St. Lawrence was one of the lowest on record. Thousands of seals were crushed in moving ice or were prematurely forced to vacate whelping patches during ice breakup, the report says.
Thousands of dead seals also washed ashore Cape Breton in 1998 and 1999, when there were light ice conditions and a weak oscillation.
Garry Stenson, a research scientist with the federal Fisheries Department, said they've witnessed poor ice conditions over the last several years in the North Atlantic.
It's estimated that up to 80 per cent of the seal pups died last year as a result of meagre and thin ice, according to the department.
But he says the department has been aware of the phenomenon and its consequences for years, factoring it into assessments and the management plan for the annual seal hunts off northern Newfoundland and Nova Scotia.
He says it may be years before the true impact of bad ice is seen in the overall population, which has risen over the years and now sits at just below eight million.
"The one safety that this population has is that they're relatively long-living and they pup over a number of years," he said from St. John's, N.L.
"So if you have one or two bad years, you still have lots of other years that are contributing to it."
Johnston said researchers will have to do assessments in the coming years before they know how much ice conditions are affecting the population.