A rare beaked whale found on a South Australian beach in February has left scientists baffled after it was discovered with two mysterious extra teeth.

The female juvenile died by the time it was discovered on Waitpinga Beach near the tourist town of Victor Harbor, prompting a team from the South Australian Museum in Adelaide to examine the mammal.

South Australian Museum collections manager David Stemmer examines parts of the whale's skull. ( ABC News: Tom Fedorowytsch )

"It was a very windy day when we went down there, and we were walking into driving rain and we could see that it was a beaked whale," senior research scientist Doctor Catherine Kemper said.

"As we were doing the dissection, after we'd done our measurements and photos, we started to the look at the jaws because that's one of the distinctive parts of a beaked whale.

"They were very odd. I didn't know what it was, because these teeth were something I had never seen before."

Beaked whales live in deep ocean waters and are rarely seen alive by humans.

The teeth in female whales are not usually erupted above the jawline, but this whale had two small and pointy teeth.

"My mind was thinking, 'do we have something new here?'," Dr Kemper said.

The situation became a little clearer after the whale carcass was brought back to the museum's maceration centre, where the skull was stripped and cleaned by bacteria in vats of warm water.

Collections manager David Stemmer pulled out the small tooth and made a surprising find.

"I discovered a bigger tooth underneath, which is the tooth of Hector's beaked whale," Mr Stemmer said.

Teeth pulled from the beaked whale's skull. ( Supplied: South Australian Museum )

"It was still exciting, and although we now knew we had a species we know, it's a species we don't get very often and it's only the third specimen we have collected here in South Australia."

The team contacted colleagues at museums all over the world, including the Smithsonian Institute in the United States, but has not found an answer for the two vestigial teeth.

They are not believed to be a deformity, but may be an evolutionary throwback.

Dr Kemper said because the whale had been collected, cleaned and catalogued by the South Australian Museum, scientists may yet figure out the reason and learn more about the elusive species.

"The more we know about our animals, the easier it is to conserve them," Dr Kemper said.

"Without that knowledge, it's just very difficult to know what's going on and to monitor whether they're doing alright."