The 25th annual census of southern right whales in the Great Australian Bight has revealed a significant drop in their number, defying the predictions of marine scientists.

Researchers yesterday counted 73 whales around the Head of the Bight in South Australia, and 15 at Fowlers Bay, a sharp decline on the total of about 200 recorded at the same time last year.

The monitoring effort is currently two and a half months into its three month schedule.

Lead researcher Claire Charlton, from Western Australia's Curtin University, said while peak calving season was last year, she was not anticipating a drop-off of this magnitude.

"Now is the time you would expect to see the peak numbers," she said.

"Some of the factors that can cause a low number could include natural variation, climatic conditions and prey availability.

"Increased water temperature in Antarctica could reduce the krill production and consequently reduce the food availability."

Ms Charlton said the decline would require further work to determine the exact reasons for it.

"This is a really good example why it's really important to continue monitoring like this and monitor annually to be able to detect these trends."

The survey collects data over 14 weeks, and researchers use photo identification and underwater acoustics to keep track of the whales. ( Claire Charlton )

Researchers reassured by overall upward trend

The census was first carried out in 1991 to keep track of the whales' breeding cycle, which re-starts every three to four years.

Ms Charlton said, despite this year's observations, the overall trend is a positive one, and the population is continuing its recovery since whaling bans came into effect.

The monitoring effort is two and a half months into its three-month schedule. ( Claire Charlton )

"What we've been able to see through this long-term monitoring program is that the population of southern right whales at the Head of the Bight is increasing, and it's thought that they're increasing at the maximum biological rate which is around seven per cent per year," she said.

"This is the recovery rate for southern right whales in Australia and around the world."

But Ms Charlton said the animals were still considered to be an endangered species.

"There's still only less than 3,000 southern right whales in the Australian population," she said.

The survey collects data over 14 weeks, and researchers use photo identification and underwater acoustics to keep track of the whales.

"We can recognise the individual whales using the unique patterns of callosities on their heads and by re-sighting these animals over time, we're able to determine their calving intervals, their migration rates, their age of sexual maturity," Ms Charlton said.

"That information is what informs us about the recovery of the population."