The Ministry for Primary Industries (MPI) is investigating how two types of bacteria could be linked to high death rates of salmon in the Marlborough Sounds.
A salmon farm in Waihinau Bay has had higher than normal rates of fish deaths in summers since 2012 and MPI said it was working closely with the country's salmon farming industry to investigate the deaths.
MPI response manager Chris Rodwell said it was believed a number of factors were contributing to the deaths, including higher sea temperatures and water flow.
"It's a pretty complicated picture, we're still determining exactly what factors may or may not be involved and certainly these two bacteria - New Zealand Rickettsia-like organism and Tenacibaculum maritimum - may possibly play a part in these fish deaths.
"Rickettsia are very small bacteria, they live inside cells. Tenacibaculum maritimum [is] a bacteria that causes ulcers in the skin of fish.
He said the rate of the fish deaths was commercially sensitive, but the affected farmer had seen a steady increase in numbers of fish deaths over the summer period over the last three years.
"That's concerning and obviously where MPI has come in," he said.
Mr Rodwell said there had been no reports of unusual mortality in other fish farming operations, but further sampling and monitoring of other farms would take place.
He said the bacteria could cause disease in fish but did not affect people.