COMMERCIAL fishermen in the Lakes and Coorong are concerned a recent government seal count is misleading.
Department of Envrionment, Water and Natural Resources staff have conducted regular counts along the channels, Murray Mouth and barrages since August.
The most recent scientific count in early November found five long-nosed fur seals on the Goolwa and Tauwitchere barrages, down from the initial count in early August of 102.
Fisher Glen Hill, Coorong Wild Seafood, Meningie, has organised a community count as he believed most of the seals were in the Goolwa channel and the Lakes where DEWNR was not monitoring.
"DEWNR is trying to downplay this, everything has been about minimising as opposed to recognising the issue for what it is - that is why we decided to do the seal count," he said.
"We figure they're probably counting about 2 per cent of the area; you can't just dawdle across the barrages and count some seals and say that's what's in the area.
"The data is clearly crucial to understanding the numbers, if the government is minimising it or inept in their counting, then whoever is making the decision is being fed this information and it's wrong information."
Meningie fisherman Tim Richards also believed the latest figures were misleading.
"The fishermen did a seal count about two weeks ago and there were 45-50 of them," he said.
"At this time of year they go back out to sea to breed.
"This happened last year and they will be back in force soon again I would say."
Mr Richards said the lower number of seals was influenced by the lower, warmer water, but did not allow the fishers any respite, as it was also a slower fishing period.
DEWNR chief executive Sandy Pitcher said seal numbers fluctuated naturally in all coastal waters throughout the year, with numbers peaking during winter months and then declining in the lead-up to the breeding season in December.
"DEWNR staff have been conducting a count every two to four weeks in the Mundoo, Goolwa, Barker Knoll and Coorong channels," Ms Pitcher said.
Ms Pitcher said the count was one of a number of studies underway into long-nosed fur seal behaviour, both in the Coorong and throughout the state.
"SARDI scientists are using satellite tags to track a number of long-nosed fur seals, including a juvenile seal from the Coorong that moved between the Coorong and Port Elliot on a number of occasions," she said.
"DEWNR staff have also installed wildlife cameras on the main pelican rookery island in the Coorong, and we are pleased to report that breeding is going well and the cameras have not recorded any interactions between pelicans and seals at the colony."
Mr Richards said the camera footage only showed a small area and was not an accurate representation of seal activity and behaviour in waters coming up to Kingston.
"The seals haven't gone up to the southern lagoon (where the pelicans are) because it's too salty for them at this time of year," he said.
"In winter when the water freshens up we'll see more interaction between the seals and pelicans.
"At the moment pelicans are still turning up with bite marks in them."
Mr Hill said the community seal count was an independent process and open to any one to have a look, with another one scheduled for November 28.