Senior veterinarian Dr Andrew Whale warns Campylobacter, which is found on nearly all Australian farms, is an endemic issue is threatening the profitability of the sheep industry.

Australia is the world's largest exporter of sheep meat, contributing $5.23 billion each year to the economy, so Dr Whale says it is critical to protect flocks to ensure farmers get more lambs on the ground particularly during the tough conditions of COVID-19.

"Campylobacter is an underlining issue greatly impacting farmers' bottom line which they aren't usually aware of," he said.

"I believe most maiden ewes in Australia should be vaccinated against Campylobacter."

Dr Andrew Whale said while the risk varied from year to year and from property to property, studies showed vaccinating maiden ewes against Campylobacter could increase lambing percentages by an average 9 per cent.

"The more devastating side of Campylobacter are abortion storms ... while they are less common, producers lose up to 40 per cent of their lambs and this has a huge financial and emotional impact."

Victorian farmer Gordon Brown, 64, has learned through harsh experience the effects of not vaccinating for the bacteria.

About five years ago he experienced a "horrible birthing period" with composite ewes he bought from Harden and introduced to a mixed-farming operation at Shelford, Victoria.

"We had a lot of deformed and premature abortions; it severely affected the breeding program and we had department vets trying to find out what was going on," Mr Brown said.

"It was suggested I try a vaccine that was fairly new at the time but it wiped out the problem for us."

Mr Brown, who has 2500 ewes and 740 maidens this year, said he would never take the risk of joining young ewes without vaccinating with a product like Coopers Campyvax.

"The market in the sheep industry is very strong at the moment and I'm seeing some of the best returns I've ever seen," he said.

"The problem is sheep numbers are down which is why one of my main objectives on the farm is to increase the survival rates of my flock.

"Each sheep that survives equals a saving of around $150."

There are two strains of Campylobacter that are known to cause lamb abortions with 95 per cent of Australian farms testing positive for at least one strain of the bacteria.

It presents itself in the intestines of healthy sheep and can be spread in faeces, urine and aborted foetuses. This leads to contaminated pastures, water sources and therefore the ingestion of the bacteria by previously unexposed sheep.

Infected ewes appear healthy and productive and may only show signs of Campylobacter when they don't produce a lamb.

Initially, Campylobacter was only thought to be an issue in cool, high rainfall regions in Victoria, Tasmania and southern parts of New South Wales, however, now experts are seeing infections in drier, mixed farming and pastoral areas across all of Australia.

Dr Whale, Senior Veterinarian and Clinical Lead at Livestock Logic, Hamilton Victoria encourages producers to consider the risks associated with not vaccinating and to be aware that some flock management practices increase the likelihood of Campylobacter being an issue.

Producers should be aware of the following practices when it comes to Campylobacter:

- Joining maiden or ewe lambs

- Trail feeding pregnant ewes

- Cell grazing pregnant ewes

- Containment feeding pregnant ewes

- Buying / transporting new ewes onto the farm