New South Wales Department of Primary Industries (DPI) staff sampling freshwater fish between Bourke and Brewarrina made the discovery earlier this month and laboratory testing has now confirmed the diagnosis.
Golden perch, spangled perch and carp in the same area were also observed with signs of red spot disease.
Aquatic biosecurity manager for NSW DPI, Jane Frances, said Epizootic Ulcerative Syndrome - more commonly known as red spot disease - showed up as red lesions or deep ulcers on the skin of infected fish.
"If caught, severely ulcerated fish should not be eaten or thrown back into the river. This includes those below the legal minimum size," Ms Frances said.
"They should be quickly and humanely euthanased by removing the head and be buried away from waterways.
"Healthy fish with no sign of red spot disease can still be caught and consumed."
Ms Frances said red spot disease had been reported in a number of coastal freshwater catchments this year, but this was the first confirmation in a western draining NSW river.
"Previous coastal outbreaks have been associated with acid water run-off, particularly after heavy rain following a prolonged dry spell," she said.
"At this stage we don't know the reasons for the inland outbreak.
"NSW DPI staff will continue monitoring the Darling River and other inland waterways where red spot is suspected."
Red Spot Disease on Darling River Fish
AUSTRALIA - Red spot disease has been found for the first time in inland NSW waterways following confirmation of the fungus on samples of bony bream from the Darling River.