Researchers have been using unmanned aerial vehicle technology and "photogrammetry" to visually access and map sea lion colonies in the Great Australian Bight for the first time.

National Parks and Wildlife Service South Australia (NPWSSA) hold the pup counts every breeding season in partnership with Parks Australia.

The sea lions have been nominated to have their conservation status under the 'Environmental Protection and Biodiversity Conservation Act 1999' uplisted to "endangered".

NPWSSA Western Eyre Peninsula marine coordinator Dirk Holman said every year, researchers have had to overcome the challenges of sheer cliffs and isolated rocky islands to count new pups.

New technology, he said, allowed researchers to find about 300 per cent more animals compared to earlier results from traditional cliff top surveys.

"The information gathered through the survey provides critical insights into how this threatened species is faring and how park managers can address existing and emerging threats," he said.

"This year, using the combination of drones and photogrammetry software, we can comprehensively 'see' colonies along the Bunda Cliffs for the first time; we can look around headlands, behind rocks and into caves, meaning pup counts are more accurate.

"These results are really encouraging and shows that the more cutting-edge survey method is improving count accuracy."

Researchers at the Bunda Cliffs complete three surveys every breeding season, photographing between 16 and 23 colonies each time.

At Nuyts every island is surveyed twice during the breeding season and also complete traditional ground counts of pups.

Mr Holman said the Australian sea lion was one of Australia's rarest seal species with population recovery is hindered by factors which included an 18-month breeding cycle, high pup mortality, and extreme female site fidelity, where females only return to their colony of birth to breed.

"This means each colony is essentially a closed population, where declining colonies will not be replenished with sea lions from other colonies," he said.

"Therefore, it's vital that we continue to monitor their numbers."