Up to a tonne of Hazelwood Pondage barramundi have been removed and euthanased amid concern for their health and survival.
Last week authorities used electrofishing techniques to check on the iconic species' condition, removing the smaller fish and those not coping with the drop in water temperature since the Hazelwood Power Station's closure.
"We really thinned numbers out to have the majority of the larger fish make it through to summer," Victorian Fisheries Authority chief executive Travis Dowling said.
"We're taking every possible step we can to still have a fishery there for summer."
Mr Dowling said there were still 3000 to 4000 barra in the pondage and he was confident the majority were in an area heated by aquifers, now sitting at 23 degrees, down from about the mid-30s when the Hazelwood Power Station was in operation.
It's understood the critical level for barra is below 15 degrees.
The authority also held concerns about the food source for the barra, with cichlids and tilapia perishing in the cold.
Mr Dowling said there were still a remnant number of those fish.
He said the fishery was not a lost cause and there was a Melbourne University study underway to look at options for keeping the waterway at the required temperature into the future.
"We'll continue to work as positively as we can for the fishery. It's been a really great success for the Valley," Mr Dowling said.
"We estimate more than 20,000 people have fished for the barra and we'll do everything we can to provide that experience for the future."
Seven thousand barramundi were stocked into the pondage proper last year as it had the warmer temperatures needed to sustain the species, because it was used as a cooling system for the Hazelwood Power Station.
But temperatures at the historically toasty pondage began to drop following the station's closure on 30 March.
The fishery has been hailed as a major tourist boon for the Latrobe Valley, with an independent survey finding an up-to $800,000 economic benefit over a four-month period.