The San Diego Zoo has about 4,000 animals — all carefully catalogued.

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 storm-water 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. He looked at the machine operator.

“I just kind of made eye contact with him,” Calvano said. “He knew right away that I had heard something big.”

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. Meanwhile, work on the storm-water project resumed.

Paleontologists had expected that digging at the site, tucked just inside the zoo fence between California 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.

“A lot of times the skull gets separated after the animal dies,” Calvano said

There have been older fossils discovered in the region, some of which are on display at the museum. Among them: a femur found in Carlsbad from a duck-billed dinosaur that roamed the region 75 million years ago, and portions of a sea cow found in Chula Vista that were dated at about 3.5 million years old.

Still, the discovery of the whale fossil is additional proof that despite the civic self-image of San Diego as a place where everything is new, the truth is somewhat different.

“The people are new,” said Sarah Siren, the museum’s paleontology field manager on site. “The whales have been here the whole time.”

tony.perry@latimes.com