He was told this was partly due to scarcity of food for the fish in the ocean, and rising temperatures.
There were also fewer people fishing in the harbour.
This would be helped next season with a new fishing area once the Fryatt St asbestos sheds were removed.
"Port Otago really are coming to the party with that."
Otago Fish and Game Council president Ian Hadland said its salmon monitoring in Otago rivers also showed a "poor season".
"Nobody is really holding out a lot of hope.
"We've only heard of a few catches."
This was due to many factors such as food supply and ocean temperature, Mr Hadland said.
"There is a lot going on at sea which we don't understand. River fisheries haven't had returns like we would expect."
As to what would happen in future seasons, it was "crystal ball stuff", he said.
"We just need to keep a little bit of hope."