A representative of Victoria's pork producers fears the temporary suspension of a Bendigo-based agency could herald its permanent closure.
Agriculture Victoria's Pig Services Centre, which provides diagnostic, surveillance and vaccine services to producers, suspended its services on March 27.
"The Pig Services Centre in Bendigo is vital for the Victorian pig industry," Tim Kingma, president of the Victorian Farmers Federation's Pig Group, said.
He said he was told the suspension aimed to protect the health of staff during the COVID-19 pandemic.
But Mr Kingma fears this is only an excuse to close the centre permanently, as staff still have to be onsite to complete existing orders.
Agriculture Victoria says arrangements have been made with a private company to provide vaccine manufacturing and diagnostic services during the suspension.
It is understood no staff have been stood down, and continue to be paid.
"We've made sure that farmers will be able to access the type of services provided by the PSC elsewhere while the centre's operations are temporarily suspended," Agriculture Minister Jaclyn Symes said.
Mr Kingma has contacted Ms Symes with his concerns, writing in a letter that the reasons for the closure "are confusing and leave industry at risk during a time where governments have publicly confirmed the pork industry's 'essential status' and the need for industry to maintain food supply".
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He said the the centre produced autogenous, or farm-specific, vaccines, which were essential in limiting the use of pharmaceuticals on farms and thereby played a large part in bringing down antimicrobial resistance.
His own farm had seen the mortality rate drop below the industry average since using the vaccine from the centre, he said.
Without good surveillance and diagnostic work, Mr Kingma said, African swine fever - "a massive threat" - would likely affect Victorian producers.
Mr Kingma said the industry was only made aware of the shutdown on Sunday, March 29, and there had been no consultation.
Murray Plains MP and opposition agriculture spokesman Peter Walsh called on the government to reverse its decision.
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