The whale carcasses landed in Trout River and Rocky Harbour, communities on the west coast of Newfoundland.
The whale bones will be buried in containers filled with manure in Trenton, Ont., and the composting process will take just over a year to clean them.
Crews used six dump trucks of manure on Thursday to bury some of the bones, each of which has been marked with a poker chip to help the team reconstruct the skeletal structure.
According to the ROM Biodiversity team, the rest of the bones will be buried in two other containers in the next few days.
The whales were two of nine rare and endangered whales that became trapped in pack ice earlier this spring. It's believed the whales were either crushed by ice or drowned as they tried to surface to breathe.