One ship didn't realize a whale was impaled on the bow until it cruised into port last August.
Earlier in October, an endangered blue whale and its fetus washed ashore in San Mateo County. The National Marine Fisheries Service says so far this year six whales have been struck by ships -- three were endangered species.
"The hemorrhaging and the breaking of the vertebrae in the whale are all consistent with ship strike injuries," says Jackie Dragon from Pacific Environment.
The U.S. Coast Guard says it is seeing a change in shipping patterns.
"They're headed out to the 24 mile line as fast as possible," says U.S. Coast Guard Lt. Cmdr. Drew Steadman.
And the ships are traveling down shipping lanes that run right through three national marine sanctuaries.
"No one would ever choose to put a national sanctuary on top of a busy airport, SFO, but that's essentially what we have," says Dragon.
At a meeting to address the problem the Pacific Environment, an oceanic conservation group, suggested a speed limit of 10 knots or about 15 mph to give the whales enough time to get out of the way. Most ships travel up to 25 knots as they approach the San Francisco Bay.
Representatives of the shipping industry declined to talk on camera, but they say restricted speeds to 10 knots would definitely affect their tight delivery schedules.
"They all have a very complicated logistics chain, so it's planned very carefully and disruptions of it are problematic," says U.S. Coast Guard Capt. Patrick Maguire.
This is part of the Coast Guard's "port access route" study which has a goal of using public input to improve safety for both the ships and whales.