SAN DIEGO — The San Diego Zoo has about 4,000 animals — all carefully cataloged.

For at least a few more days, it will have one more that officials didn’t even know existed until Thursday when an excavating machine digging a hole for a stormwater runoff tank made a distinctive scraping sound.

Gino Calvano, a paleontologist at the San Diego Natural History Museum, acting as a fossil monitor on the project, heard the sound and came running.

Calvano realized that the machine’s metal scoop had scraped a large fossilized skeleton. A quick inspection determined the skeleton was that of a whale from about 3 million years ago.

Work was stopped and, in accordance with state law, paleontologists from the nearby museum in Balboa Park quickly assembled.

By Friday, the squad was carefully chipping, dusting and digging in preparation for the skeleton to be encased in plaster and taken back to the museum for additional study.

Paleontologists had expected that digging at the site, tucked just inside the zoo fence between California Highway 163 and the park’s Polar Bear Plunge, would uncover some shells, maybe some shark teeth. But finding a whale fossil, particularly one 20 feet long and largely intact, was unexpected.