Early findings indicate that the whale is a minke whale and that it was not killed in the San Francisco Bay, according to the Marine Mammal Center in Sausalito and the Long Beach branch of the National Oceanic and Atmospheric Administration.
Both agencies said the company that operated the ship, Norton Lilly International, is cooperating with the investigation by answering questions, arranging the removal of the carcass from the harbor, and compiling a report that will be submitted to NOAA within a month.
That report will indicate where the carrier's journey started and could help shed light on where the whale was hit, which NOAA spokesman Joe Cordaro said was "probably not in the immediate area of the San Francisco Bay."
Cordaro said NOAA gave official permission Thursday afternoon to have the carcass towed 10 to 12 miles offshore. Norton Lilly International was expected to contract a tow company for that removal by Friday morning, he said.
Jeff Crysel, the Norton Lilly International operation manager for the Port of Oakland, said he could not comment on whether or not the carcass had been removed by 1 p.m. Friday.
Cordaro said the preliminary NOAA investigation will focus simply on determining the species of the whale and whether or not the ship's operators saw the animal before they hit it.
The administration's enforcement division will then investigate whether the strike was unintentional, he said.
"It's a high management priority to try to minimize the strikes on these animals," Cordaro said of stopping "ship strikes", as these collisions are called.
The U.S. Coast Guard issued a reminder to boaters after the whale's body was found to be watchful for whales in the shipping channels near the Golden Gate Bridge, as the giant mammals will likely be hunting for krill, their tiny crustacean food source, in the passageway.
"It's sad for us to see something like this happen," Jim Oswald of the Marine Mammal Center said. "We encourage the public to really educate themselves about marine mammals."
The last report of a collision between a ship and a whale in San Francisco Bay was in 2008, and before that in 2006, Cordaro said. Delta and Dawn, a humpback cow and calf that got media attention in 2007 when they became trapped in and were successfully freed from the Sacramento River, were also determined from their injuries to be ship strike victims.
Cordaro said NOAA has been trying to reduce ship strikes by asking vessels in the shipping industry to slow down to 10 knots or less when they are traveling in an area that has been experiencing an influx of hungry whales.
Whales hit at 10 knots or less stand a far greater chance of surviving the collision than whales hit at higher speeds, Cordaro said.
However, he said it can be difficult for ships to travel that slowly, a land-speed equivalent of about 11.5 mph.
"To ask a ship to hold at 10 knots for its whole journey doesn't appeal to the economic aspect," he said. "It adds cost to the trip."
Cordaro estimated that the carrier ship that dragged the whale on Thursday was probably traveling at around 20 knots - standard carrier ship traveling speed - when it struck the animal.
The massive ship dwarfed the whale as it was pushed along on the bow of the carrier, which pulled into Berth 57 in Oakland around 10 a.m. Thursday.
"They are so huge, even an 80-foot animal is miniature compared to these ships," Cordaro said.
The whale has been estimated to be between 30 and 50 feet long, but Oswald said it may be impossible to ever determine how big it was because pieces of it were missing by the time it got to Oakland.
Sharks began to feed on the carcass after the ship docked in Oakland, but Cordaro could not confirm that the whale had shark bites on it when the boat arrived at port.
Officials from the Marine Mammal Center removed skin tissue samples from the carcass on Thursday, Oswald said. Cordaro said only when those samples return from lab testing in several months will it be certain what species the whale was.
Oswald said multiple specialists from the mammal center, which investigated the incident under the direction of NOAA, were "pretty confident" the whale is a minke.
That species is more prevalent in the Bay Area than in Southern California, Cordaro said.
Unlike blue and humpback whales, minke whales are not on the Endangered Species List, but are protected by the Marine Mammal Protection Act, he said.