The lowland longjaw galaxias is ranked as acutely threatened, with a status of being nationally critical.
The Department of Conservation is seeking approval to move up to 2000 fish, due to concerns about the population's long-term survival in the Kauru River.
The translocation proposal was put to the Otago Conservation Board recently and would also be considered by iwi, Ministry of Fisheries, and Fish and Game before going out for public consultation.
An environmental impact assessment by Doc freshwater ranger Pete Ravenscroft recommended the transfer, as the recent arrival of didymo into the Kakanui River catchment had greatly added to the concerns about the long-term survivalof the native species.
A worst-case scenario could see didymo causing the extinction of the population, he said.
"It is critical that this translocation process proceeds as soon as possible. It is important that the fish are transferred into didymo-free water."
Establishment of a new population had been a longstanding objective for Doc, and in 2007 it was proposed to move the fish to Big Kuri Creek.
However, the creek ran dry for long periods and a reassessment of data from that time showed the Waianakarua would be a much better site, he said.
Its habitat was similar to the Kauru's and its upper reaches were unlikely to be infested by didymo, he said.
Releasing the fish into the Waianakarua would not impact on other users, as people could continue to go fishing, swimming and take water from the river.
It was planned to translocate 1000 fish in year one and another 1000 if needed the next year.
About 350 fish had been caught recently and were being kept with the back-up population in tanks in Concord.
They were available to be relocated as soon as the proposal was cleared, he said.
The majority of fish would be collected by electric fishing from the Kauru and transported directly to Waianakarua.
The two proposed release sites were within a reach of river at the bottom of the gorge, within the Glencoe Scenic Reserve, Cosy Dell Road.
