SOUTH Australia's Giant Cuttlefish breeding colony - regarded as a natural marvel - has disappeared.

Experts and tourism operators say they are at a loss to explain why the tens of thousands of Giant Australian Cuttlefish have not appeared for their annual breeding migration.

They fear the species is in danger, saying less than a quarter of the usual numbers have made it to the shallow, rocky waters off Whyalla and those that have are smaller than usual.

This is the only place in the world that the cuttlefish gather in such large numbers to breed.

No government department, however, claims responsibility for monitoring their numbers.

The Department of Environment and Natural Resources (DENR), the Environment Protection Authority and Primary Industries and Resources SA all told the Sunday Mail they were not responsible for counting cuttlefish to ensure the species was safe.

Adelaide University ecologist Professor Bronwyn Gillanders said the cuttlefish looked to be in danger. "I have heard reports the numbers are way reduced," she said.

"Initially it was thought they were coming in late this year, but they should have been at their peak abundance in mid-to-late June. It's really hard to tell whether this is a natural phenomenon or something else."

She said more research was needed to determine the cause.

"I don't think anybody has any idea about what could be causing it," she said.

"The reason it is so concerning is that cuttlefish die after mating. A species like snapper can have a bad recruitment year but the same fish can still come back and lay more eggs.

"The cuttlefish can't come back and breed again."

Whyalla dive boat operator Tony Bramley believes they are being fished by boats targeting an area just outside the Point Lowly exclusion zone.

"We are very, very concerned because the numbers this year are disastrously low," he said.

"There is a tiny little finger of coastline out near Point Lowly outside the zone.

"I believe that's where they access the reef from the deep water. They should close that. It's been described as the best marine spectacle in the world and we're risking losing it. The cuttlefish have turned up (this year) - it's just the fisherman took them all.

"In other years the bottom was a carpet of them.

"The reef was covered but if you go out there now, there's hardly any."

Shayne Grant, a former tour operator and local diver, said locals were concerned a major tourism drawcard and ecological wonder could disappear.

"Last year they were everywhere but this year they haven't moved in at all," he said.

"Tourist numbers seem to be dropping off, too. People are finding out about it."

In an emailed statement to the Sunday Mail, a DENR spokeswoman said: "PIRSA protects the cuttlefish aggregation with a fishery closure across False Bay.

"DENR is considering advice from the local community to develop a marine park sanctuary zone in the area that will provide extra protection to both the cuttlefish and the habitat they depend upon. DENR has heard the concerns expressed by tourism operators that there are fewer cuttlefish near Whyalla this year, but does not monitor their numbers and is not aware of concerns around a particular fishing location."