Spawning runs can turn Thredbo and Eucumbene rivers black with trout, but for two seasons the rainbows, highly prized for their aggression in taking a lure, have been missing in action.

NSW Fisheries has called in Dr Michel Dedual from New Zealand's Department of Conservation, who has been studying similar issues at Lake Taupo, for advice.

Dr Dedual will join fisheries, national parks, water managers, acclimatisation societies and tackle shops to assess the problem.

Monaro Acclimatisation Society president Steve Samuels said Gaden Trout Hatchery on the Thredbo River trapped and counted fish.

''In a normal year the trap operates for about two weeks and takes about 2500 fish and that will give them enough eggs to do all their stocking,'' Mr Samuels said. ''Last year they had the trap in for the whole season and we only got 600 rainbows.

''We are talking to [NSW] Fisheries, because it is a big deal up there, it brings in a lot of money.

''For [the previous] five years there's been good rainbow catches and runs; the brown trout hardly showed up at all.

''But in the last two years when the rainbows went missing, the browns showed up and they have been very, very strong.''

NSW Department of Primary Industries senior fisheries manager Cameron Westaway said that while the fishery generated an estimated $100 million annually, the lack of rainbow trout was no cause for concern.

Dramatic changes in lake levels over the past 10 years from drought, power generation and irrigation could be causes.

''That means the whole food chain in the lakes can change,'' Mr Westaway said.

''Daphnia, a small crustacean, the rainbows go deep and can sit on them, that's the reason they get that lovely red flesh in those lakes, which can make them hard to catch.''

He said as he was a Canberra boy, he had fished Lake Eucumbene for many years, in fantastic and lean seasons, including a decade ago, when a working group was formed to address a similar problem to today's scarcity of rainbow trout.

'The people I respect have rung me with concerns; they are not seeing the numbers in the shallows, especially in Jindabyne. So we'll look at it.''

Another fishermen with more than 40 years in the sport, James Morgan, of Tackleworld, Fyshwick, said rainbows did not spawn as well as browns, and needed colder water.

''Fly fishermen are still up there, they still know the rainbows are there. They are probably in pretty big numbers. It has been a very hot summer.

''Fishermen are the worst people for making excuses for themselves.''