Fisheries Queensland General Manager of Habitat and Assessment Dr John Robertson said initial test results identified two conditions, red-spot disease and a parasite.
"Red-spot disease is endemic and is seen in Queensland waters occasionally," Dr Robertson said.
"In Queensland, red-spot disease usually occurs either during winter months when the immunity of the fish is lower, or following the first heavy rainfall of the wet season."
"Red-spot disease starts with a red spot, hence the name, but can develop into burn-like marks, or ulcers with red centres."
"It is typically caused by a fungus and often occurs in fish when they are under stress."
Dr Robertson said more research was needed into the parasite, which affected the eye of the fish.
"We now know that this parasite is what has been causing the cloudy eyes in some barramundi in the area," he said.
"We still have more to learn about this condition and how it is affecting fish within the area."
Additional testing is being conducted on newly received samples of other fish species, prawns and mud crabs but results are not expected for several weeks.
Dr Robertson said the temporary fishing closure would remain in place at this stage.
"The closed area is between Deception Creek at the top end of The Narrows down to Rodds Peninsula and to the outer edge of Facing Island and applies to all tidal waters including rivers, creeks and other waterways," he said.
"While the temporary closure is in place commercial, charter and recreational fishing, including catch and release, are not permitted."
Waters upstream of the Awoonga Dam wall are still open to recreational fishers and licensed commercial fishers can still operate outside the closed area.
A map of the closed area is available at www.fisheries.qld.gov.au
Queensland Health Acting Chief Health Officer, Dr Michael Cleary said seafood that showed signs of damage, deterioration or disease should not be consumed.
"As at all times, any fish that show signs of illness are not fit for human consumption," Dr Cleary said.
The closure ensures that any fish that are potentially unsuitable for human consumption will not enter the food chain.
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