It's not known if the whale was dead or alive when it was struck by the Seven Seas Navigator, said John Ford, a marine mammal scientist with the Department of Fisheries and Oceans.
"When it docked, a whale that had apparently been draped over the bulbous bow of the ship floated off," Ford said Monday, after the whale was towed to North Vancouver for a necropsy.
He said it appeared the whale was hit north of Vancouver Island on Sunday.
"If it is a fin whale, it would be the third fin whale that's come into Vancouver harbour on the bow of a cruise ship."
The first incident was in 1999, followed by another 10 years later, when that whale was believed to have been hit after it had died.
"This one appears quite fresh though, but it's still possible it was struck while it was dead."
Ford said fin whales are listed as threatened on the West Coast of Canada, but their numbers have been increasing after dwindling during the whaling era that ended in the early 1970s.
He said the presence of more fins is possibly why more of them are being hit by ships of all kinds.
"Fin whales, for some reason, are the most common large whales hit by ships," Ford said, adding the speed at which cruise ships and container vessels travel on the high seas compared to other ships could be a factor.
Ship strikes are a concern along the West Coast and other parts of the world and several studies are underway to determine how to mitigate the risk of large whales getting hit, he said.
"Fin and blue whales have been identified as being at risk in shipping lanes coming in and out of San Francisco and Long Beach, or Los Angeles, and there have been steps to try and reduce that by altering ships lanes when there are concentrations of whales in certain hot spots."
Scientists don't know how many fin whales there are, though 500 of the individual whales have been identified from their markings through photographs in the last five years, mostly on the north coast of Vancouver Island, Ford said.
Their population is likely more than double that number and Ford's research group at the Pacific Biological Station in Nanaimo, B.C., is trying to determine more precise figures.
Fin whales are the second largest whales in the world, after blue whales, about 3,000 of which ply the waters of the Pacific Coast of the United States. Ford said blue whale sightings are extremely rare on the West Coast.
Fins mature at age 25 and can be distinguished by the asymmetrical pigmentation on their lower jaw, which is dark on the left and light on the right.