The Department of Agriculture, Food and the Marine (DAFM) has said there is "no evidence" that bluetongue vaccination is associated with birth deformities ahead of the higher risk period for the virus.
Minister Martin Heydon - who authorised the import of more than four million doses of bluetongue vaccine under Special Import Licences - has highlighted that vaccination can "reduce the impact and severity of bluetongue virus on livestock".
The minister has also advised cattle and sheep farmers to consult with their vets, to decide whether to vaccinate their flocks or herds.
Sheep vaccination takes three weeks to take full effect and cattle vaccination takes six weeks.
Farmers, livestock owners and vets have been urged to "remain vigilant for bluetongue".
Sheep are more likely to show symptoms and signs of bluetongue than cattle.
Cows infected with the virus can show symptoms of fever, lameness, respiratory disorders, drooling, facial swelling, and cyanosis of the tongue.
According to DAFM the effect of cows being infected with bluetongue while pregnant can vary from no clinical signs - that is calves born clinically normal - through to abortion, malformed calves or calves born with neurological signs at birth.
However the department has said that it is important to note that "deformities usually occur if the cow is infected in the first third or second third of her pregnancy".
"These deformities will persist even if cows are vaccinated towards the end of pregnancy," it warned.
"There is no evidence that vaccination is associated with birth deformities," DAFM confirmed.
The department's advice to private vets and herd-owners is to submit aborted calves, still births or calves which are born with suspect clinical signs and which subsequently die or are euthanised, to a local Regional Veterinary Laboratory (RVL) where they can be tested for a number of diseases.
DAFM confirmed to Agriland that an aborted calf which was submitted to the RVL did test positive for the virus and demonstrated brain lesions on post-mortem examination.
The department has continued to stress that "there are no public health risks" associated with the virus.
"Bluetongue does not affect human health or food safety; meat and milk are safe to eat," DAFM stated.