South Australia's Department of Primary Industries and Regions (PIRSA) says giant cuttlefish numbers are down by 97 per cent.
Last year the department counted 63,000 cuttlefish in the Spencer Gulf waters. This year 1,811 were recorded.
South Australian Research and Development Institute executive director Professor Mike Steer said the decline was being monitored closely.
"The [giant cuttlefish] population has depleted and has likely been impacted by the algal bloom," he said.
The number is the lowest since 2013, when Pirsa recorded 13,000.
Marine biologists visited the Spencer Gulf last month to count the eggs left behind.
"Along that 8 kilometres of coastline we only found 440 eggs," Manny Katz said.
The annual gathering near Whyalla is one of the only known mass-breeding aggregations of its kind.
"It's the only place where our giant cuttlefish come for breeding," SA Climate, Environment and Water Minister Emily Bourke said.
"So we see this population as a priority to protect."
The future of the giant cuttlefish
Adult giant cuttlefish die shortly after spawning, leaving the next generation reliant on that single winter event.
"Normally when there's tens of thousands of cuttlefish and each female is laying dozens of eggs, you would expect there to be millions along the coastline," Mr Katz said.
"My team went out and jammed our heads under every single rock we could at eight sites. At some we found no eggs at all.
"It's incredibly worrying. It's probably an indicator that next year's population is going to be incredibly low as well."
Professor Steer said the one-two year life cycle of the species gave cause for hope.
"In 2013 when numbers dropped down they popped back up in a couple of years," he said.
"Cuttlefish breed one year, die, and then the resulting hatchlings make up the population next year."
Professor Steer said the harmful algal bloom was a likely cause of the decline.
"We saw those [giant cuttlefish] eggs successfully hatch last year," he said.
"Those went into the water where the bloom was present, where we'd expect to see those juveniles and sub-adults. So it's likely that it's had an impact.
"We did see a lot of fish perish as a result of the algal bloom. We need to research into the food web structure."
Mr Katz is urging the government to protect the giant cuttlefish with a formal endangered listing.
"They should be listed as an endangered species," he said.
Invertebrates Australia has made an application for the species to be listed on the International Union for Conservation of Nature Red List of Threatened Species.
"I think now there's reason to warrant them being federally listed in Australia as an endangered species, to trigger more funding and monitoring for the future," Mr Katz said.
A spokesperson for the federal government said in a statement that "the reduction in giant Australian cuttlefish populations in the Spencer Gulf is very concerning".
The spokesperson said Environment and Water Minister Murray Watt has asked that the Threatened Species Scientific Committee "urgently consider whether a listing for the Upper Spencer Gulf population of giant cuttlefish under the EPBC Act is appropriate, and if so, to undertake that assessment".
A joint research project between the state government and Adelaide University will track the Spencer Gulf giant cuttle fish population until 2028.
Research is also being conducted on how cuttlefish numbers are calculated.
That will be funded with part of the federal and state governments' $165 million algal bloom response fund.
