A Department of Primary Industries internal discussion paper, obtained by ABC Rural through Right to Information laws, reveals that an increased rate of the disease was recorded last year.
The paper links the disease to a degraded environment and warns Macquarie Harbour's low oxygen levels and complex marine environment increases the risk of disease spread among salmon.
Senior Lecturer in veterinary pathology at the University of Adelaide, Dr Stephen Pyecroft, said a degraded environment would worsen the incidence of the disease.
"You get an increased number of those bacteria if you have low dissolved oxygens, high levels of detritus, and you get into what we call an eutrophic environment (high amount of nutrients from fish waste)," he said.
"[A degraded environment] would promote the presence of mycobacteria, [with] any degrading in the environment you're going to predispose animals to infection."
