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The organisation is in the initial stages of creating a committee and management plan for revitalising the fish.
Contact Energy has also expressed interest in creating a hatchery on the Clutha River to improve numbers.
The measures came from a meeting in Ashburton at the weekend, which was attended by 120 anglers.
Fish & Game Central South Island officer Mark Webb said numbers in the Waitaki River fluctuated but were generally "very low" since a big dip in the early 2000s.
"The populations have reset themselves at a much lower level."
The reason for the decline was not yet fully understood, but could be related to their time in the ocean, he said.
"We still know very little about what they do when they’re out at sea, where they go."
The situation was the same in other important salmon rivers, such as the Rakaia, Waimakariri and Rangitata, he said.
A committee and South Island management plan were great places to start, he said.
"The mood at the end of the conference was very positive."
Fish & Game Otago officer Helen Trotter said the wild salmon population in the Clutha River dramatically decreased with the creation of dams and had remained low, but variable, ever since.
Before the Roxburgh dam was built, salmon numbers in the river were estimated at between 20,000 and 50,000, whereas recently they were as low as a few hundred and about 1000 at their highest.
"The main issue in the Clutha is they can’t reach their habitat," Ms Trotter said.
Since 2010, Contact Energy had released smolt in the river, starting at 30,000 juvenile salmon a year and eventually ramping up to 200,000, as part of its most recent resource consent.
However, these were taken from Canterbury rivers and very few survived, but a hatchery on the Clutha River itself might help this, Ms Trotter said.
New Zealand was the only place a Chinook salmon population had established outside Sacramento, California, where they originated, she said.
"Salmon are a highly valued fish and our anglers value them not just for sport, but also for harvest."
The Dunedin Community Salmon Trust released smolt into the Otago Harbour, but those salmon were probably subject to the same issues as others across the South Island, Ms Trotter said.
At the meeting, Fish & Game chief executive Martin Taylor said the organisation was "fighting a last-ditch battle" to save wild salmon.