Canada's Royal Ontario Museum will take two blue whale carcasses that washed up on the coast of western Newfoundland.
Whales on the beaches of Rocky Harbour and Trout River were among several believed to have died in heavy ice.
The towns did not have the resources to move the decomposing whales, which experts fear could bloat and explode.
"The chance to preserve, study and examine up to two skeletons is a once-in-a-lifetime opportunity," the museum said in a statement.
The museum estimates there are fewer than 250 of the creatures in the Northwest Atlantic.
The move comes after a joint agreement between the museum and Canada's Fisheries and Oceans department. It is unclear how long it will take museum scientists to remove the whale entirely from either beach.
Canadian officials earlier said it was each town's responsibility to handle the dead whales.
Trout River Town Clerk Emily Butler says the 25m (81ft) whale near the town's boardwalk is bloated with methane gas.
She fears as temperatures rise, the whale corpse would start to reek or potentially explode from the build up of gas.
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