Clean Seas has suffered a setback in establishing its operations in Fitzgerald Bay with 40,000 fish being lost because of a mechanical failure.
The fish were being transported from Arno Bay in a tanker when an oxygen pump failed, causing the loss of thousands of fingerlings, which were unknowingly put into the water and later had to be recovered.
One of the dead fingerlings was found by a local fisherman who passed on a photograph to recreational fisher Nick Antonio, who subsequently raised the issue with Clean Seas.
Clean Seas chief executive officer Rob Gratton said the incident wasn't something which would usually be reported to the community.
"There is no impact on the community from these things happening. We are certainly committed to keeping the community updated where our activities have an impact on them," he said.
"It is unfortunate because it has a cost-of-production impact, but it doesn't affect our ability to supply the market or the overall number of juveniles that will be put in the water.
"The fish will be replaced in the next run. We always build in some contingency for such events."
But Mr Antonio says Clean Sea, who are based in Port Lincoln, should have been more open with the community, with the incident being uncovered through third-party sources.
"A photo from the community alerted me to the incident," he said.
"It took an email to Clean Seas, the Whyalla City Council and PIRSA to uncover what happened, I would have hoped that this would have been reported to the community and PIRSA right off the bat."
The Primary Industries and Regions Department (PIRSA) said they had been informed of the incident by Clean Seas, but it was not a reportable mortality event under the Aquaculture Regulations.
"As such, any other inquiry about this matter should be directed to Clean Seas," said a spokesman.
Whyalla City Council chief executive officer Justin Commons declined to comment on the incident.
Aside from the initial setback, Mr Gratton said the juveniles now in the water had been performing well in terms of growth and survival.
"It's in line with what we'd expect to see at our other farms," he said.
"We have continued the recruitment process, we're up to 14 employees at Fitzgerald Bay and we are seeking another seven employees in the Upper Spencer Gulf."