The whale was first spotted floating in the bay on Friday and by Saturday the carcass had washed up along the rocks near the Oakland International Airport.
On Tuesday the Marine Mammal Center had the whale carcass towed to Angel Island so they could perform a necropsy.
Scientists say the carcass was badly bruised and there were several fractures in the animal's skull. Experts believe the adult female was hit by a ship or large boat.
RELATED: Dead whale washes up on Angel Island State Park in San Francisco
"The whale is on an inaccessible beach," said Alex Luscutoff, the supervising ranger at Angel Island State Park. He spoke to ABC7 News by phone from the island.
He is pleased the park can provide space to research the whale but says visitors need to stay away.
"We have had visitors that have tried to go down to access the beach where the whale is located and it's just inaccessible. It's on a very very steep -- almost cliff-like terrain, and it's not safe to try to come out and view it," Luscutoff added.
The Marine Mammal Center hopes their research will protect animals and their habitats in the future.
Click here for a look at more stories and videos about whales!