Combined Vet Services vet Karen Nicholson, of Gore, said she had heard "horrible" stories of the disease killing cows in southern Southland.
The disease had been "particularly bad" this season.
"This is an abnormal pattern."
Cows ate the bacteria and if they were under stress, struggled to fight it in their guts and became sick, often dehydrated with acute diarrhoea.
"The worst-case scenario is that your cows die."
Salmonella bacteria could enter a farm by an infected cow carrying it on the property.
"When the carrier animal get stressed, they start spreading but there is a little bit of the unknown."
At a recent DairyNZ field day in Eastern Southland, farmers asked Dr Nicholson if the wet spring attracting more waterfowl to farms could be the cause of the disease’s spread.
"We don't know.
"We think that maybe that birds are responsible but we also think that there's probably carrier cows as well ... we just don't know."
Ministry of Primary Industries had launched a "salmonella survey" to investigate why the disease was on some farms and not on others.
A vet could provide the survey to any dairy farmer who wanted to contribute, whether they had salmonella on their farm or not.
Cows could be vaccinated for salmonella and need two jabs if they had never had a shot before.
The ideal time for the vaccination was in April or May, Dr Nicholson said.
"You don't want to do the second shot too close to dry off because it can make the cows feel a little bit average for a couple of days."
Biosecurity New Zealand animal health surveillance principal adviser Jonathan Watts said Southland and South Otago had been experiencing a significant outbreak of salmonella in cattle since spring last year.
Salmonella could cause significant sickness and death, impact production and welfare in cattle and could cause sickness in humans.
"We would like to understand the risk factors that have led to this outbreak to help mitigate future outbreaks and to reduce the impact of outbreaks in the future."
Federated Farmers Southland vice dairy chairman Kass Rauber, of Hedgehope, said there more than 100 cases of salmonella on dairy farms in Southland this season.
In a normal year in Southland, about a dozen farms had the disease in their herd during a season.
The disease hit cows hard, especially during calving.
Southland was extremely wet in spring and the impact was ongoing.
"It will take a long time to repair the damage from this spring."
