VetSouth veterinarian Vincent Sharp said the practice had been seeing more cases of Salmonella Brandenburg this year than in previous seasons.
Dr Sharp said outbreaks followed a drop in immunity.
When the disease first appeared some years ago, farmers were vigilant in vaccinating ewes, but in recent times had relaxed vaccination programmes and the present outbreak could be attributed to that fact, he said.
Even if ewes were vaccinated, mobs could contract the disease, but the effect would be less than if they were not vaccinated, Dr Sharp said.
It was important aborted fetuses were picked up as soon as possible as seagulls could pick up the material and spread the disease to other properties, he said.
Dr Sharp said the disease had not only struck pregnant ewes, but was also prevalent in dairy cows.
"We have been busy calving rotten calves," Dr Sharp said.
While he was unsure how many areas were affected by the disease he believed it was "widespread".
The main concern for dairy farmers was that staff would pick up the disease when calving the cows.
But if the cows were calved in a dairy shed then disinfectant, gloves and hot water would be on hand, he said.
He urged farmers to carry, gloves and disinfectant on their farm bikes when out in the paddock to avoid becoming infected themselves.
Edendale Veterinary Clinic vet Claire Hunter said there were definitely more cases of Salmonella Brandenburg in Southland this year.
Dr Hunter agreed immunity to the disease was waning.
However, it is possible to treat ewes after they have aborted by giving them antibiotics.
Gribbles Veterinary Pathology Invermay pathologist John Gill said it was hard for the organisation to determine if there was a rise in the number of Salmonella Brandenburg cases as they were only sent between 30 to 40 per cent of total cases by vets, for confirmation.
One of the difficulties with dairy cows contracting the disease was that they usually carried the calves full-term and they then had to be calved.
"They don't seem to expel them [rotten fetuses]," Dr Gill said.
Waikoikoi farmer Stephen Lietze said his ewes had been hit by the problem this year and he estimated between 20 to 25 ewes had died and about 70 had aborted lambs so far.
"It's not as bad as some guys have had - it could have been worse," Mr Lietze said.
Vets advise farmers to spread ewes out in paddocks to lessen stress, but Mr Lietze said that often traded one problem for another.
He said if ewes got too much feed they could have bearing problems.
"So, it's a trade-off," he said.
Mr Lietze had stopped vaccinating, because there was more than one strain and vaccinated ewes still contracted the disease.
This was the third time ewes on Mr Lietze's property had had the disease, he said.
