However, it has said that growers can seek special consideration if they believe they have been harshly hit, by writing to the South Australian government.
A report on ABC said the model for the industry had been changed from a per hectare basis to a per lease basis.
Some oyster growers were alarmed that their fees could rise by 450 per cent.
Acting executive director for aquaculture, Heather Montgomerie, told ABC that lease holders were consulted before the change.
"We're talking about cost recovery, we're not talking about a rent based on the value of what they can earn from those leases and the fact that it does cost us the same amount to look after a small lease as it does a large lease," she told the network.
Oyster Growers Alarmed over Increased Fees
AUSTRALIA - Oyster growers in South Australia will face higher costs because of a change in the aquaculture recovery model, according to South Australia's Department of Primary Industries.
