ABA chief, David Mazengarb, says the company is making every effort to recover up to 32 damaged sea cages which broke loose.
Having just seen external administrators hand the company back to the board he says it is an unexpected set-back for the team.
"It is quite serious for the company and we've devoted a lot of time and effort over the last 24 hours to securing the site and the position," he told Gippsland Aquaculture Industry Network.
"Certainly it's very disappointing at this point in time to lose those sea cages and infrastructure in the fashion that we have done."
The company fears losses could run as high as $3-5 million.
Some of the damaged cages have been found ashore at West Waldegrave Island, known for its sea lion population.
Mr Mazengarb says he is sure the plastic cages will not harm the wildlife there.
"We treat that quite seriously and our teams are in the water to assess what the damage is and take what immediate corrective action they can to ensure there's no danger to the environment or the sea life in the vicinity."
Green groups claim they have been predicting this for years and trying to highlight the risks.
Former Greens MP Sandra Kanck stressed that the off-shore abalone farming should never have been allowed.
"It very much is a case of 'I told you so'. Five years ago we said that this was going to happen, it was the wrong place for it and the fact that these are now being washed up in a sea lion colony is absolute proof of the fact that this should never ever have been able to be located there," she was cited as having said.
Some farmers are counting the cost of crop damage from weekend storms.
The Eyre Peninsula was hit by winds of more than 100 kilometres per hour and local farmers have suffered extensive crop damage.
Storm Causes Over $3 Million Worth Of Damage
AUSTRALIA - Millions of dollars damage has been feared done to the Australian Bight Abalone (ABA) farm off the South Australian coast at Elliston by high seas and wild weather over the weekend.
