Last week people were urged not to eat lampreys, or kanakana, from the river, near the Mataura township, after samples found fish with red fins and contusions on their bodies.
Ministry of Agriculture and Fisheries was testing the fish and had provisionally identified the presence of a bacteria, aeromonas salmonicida, but it would take up to four weeks to identify the correct strain affecting the fish.
Different strains of the bacteria affected different fish but they did not affect human health.
There was a possibility it was in other rivers in other Southland and there had also been an unconfirmed report of dead lampreys on the banks of the Clutha River.
However, there had been no reports of problems within the trout fishery in the Mataura River, with anglers on opening day of the fishing season on Saturday not noticing any obvious disease or problems, Southland Fish and Game officer Zane Moss said.
"It's a developing story. Unless it is observed in trout there is not any cause for concern. We're optimistic for trout or other species."
Otago Fish and Game officer Morgan Trotter said the news that the bacteria was out there was quite a concern. "It could be didymo, but worse."
Environment Southland aquatic ecologist Andy Hicks said the bacteria had caused problems in agriculture around the world but had not been detected in New Zealand before.
"The bacteria has affected trout, salmon and eels overseas so it's capable of infecting whitebait through to eels."
Just what sort of impact it could have on any fishery in New Zealand depended upon the strain, but it was causing lampreys to die off, he said.
It was not yet known what caused the outbreak. It could be a response to environmental conditions or it could have been spread by the ocean-going lampreys.
"It is in Australia and has been identified as a potential risk."
The council was developing a response plan to deal with the outbreak and was calling on anglers to keep an eye out for anything unusual while fishing, call MAF on 0800 809 966 if they did, and wrap affected fish in plastic, then in paper and put them on ice.
Fish and Game are investigating the discovery of about 30 fish left on the bank of the Diamond Creek at Glenorchy at the weekend, some of which had been filleted.
Officer Morgan Trotter said there was a single-fish bag limit on the creek so it was a major breach of regulations.
He said anyone with information should contact fish and game.
