Marine biologists said it was too early to tell what killed the 4m beaked whale.
The three to four-metre-long animal was found dead on Redhead Beach, south of Newcastle, this morning.
Marine experts have been called in to examine the whale and take specimens.
Organisation for the Rescue and Research of Cetaceans in Australia (ORCCA) president Ronny Ling said the find was extremely rare.
"It's a deep sea animal called a beaked whale," he said.
"We're yet to identify the exact species but what we can tell you about these animals is they are rare animals.
"You normally only find them when they wash up or when they strand and they are vey, very seldom seen at sea, so it has great scientific value there.
"It's rare everywhere and not just Australia, worldwide.
"Some of these species are only known from a handful of strandings."
Researchers from the Australian Museum have shown interest in the find.
Marine biologist Elise Bailey said the animal would be preserved for researchers at the Australian Museum.
She said she had never seen a beaked whale in her 20 years of study until today.
"You don't normally see a beaked whale come into these waters; it's an oceanic animal and it's [usually] going to be way out in very deep offshore waters," she said.
She said it was too early to say why the whale died.
"It could be sick, it could be old, it could have had some trauma," she said.
"It's going to the museum, so we are just going to move the animal and we are going to get them the material that they want to look further into what's happened."
ORCCA vice-president Shona Lorigan said the beaked whale was a "very cryptic species".
"They disappear very, very quickly," she said.
"So for a very, very long time not much has been known about them and so every time we even find one that is dead on the beach, it is a treasure trove for the scientists."
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