National Marine Fisheries Service spokesman Brian Gorman said an investigation was under way because it's illegal in most cases to shoot any kind of sea lion.
West Seattle residents have reported at least one other sea lion carcass was floating in Puget Sound, Gorman said.
At least one sea lion is found dead near Seattle each year, but five was an unusually large number, Gorman said.
"It's impossible for us to say right now where these animals were shot," he said. "Or even if it was one shooter."
Wildlife biologists believe the animals were dead for a week or two before their carcasses came to shore in several places.
Seattle has a love-hate relationship with California sea lions, which are accused each year of eating too many threatened spring Chinook salmon.
"Some people don't like them," Gorman said of the seals, pointing out the irony that sport fishermen want to do exactly what the sea lions do: eat salmon.
The Oregon Department of Wildlife estimates there are as many as 300,000 California sea lions along the Pacific Coast. Another group of sea lions was found shot to death near Seattle last March.
Gorman said it's legal to kill a sea lion if it's threatening your life or your safety. Some Indian tribes also have permits to kill the mammals.
West Seattle is on the Peninsula across Elliott Bay from downtown Seattle.
