Three cases of illness from Japanese encephalitis virus have been confirmed and another 16 are being investigated in an unprecedented outbreak across four states of Australia, health authorities say.

Transmission of the mosquito-borne disease, once confined to the Top End, is so widespread it could entrench the virus, making it endemic, warns arbovirus expert Adjunct Professor Scott Ritchie.

The Federal Government has declared the spread to be a communicable disease incident of national significance and has sent Japanese encephalitis virus (JEV) vaccines to state and territory public health units to inoculate at-risk people, including piggery workers.

Since the first infections were detected in pigs at the end of February, some 42 piggeries have confirmed cases spanning NSW, Victoria, Queensland and SA, Minister for Agriculture David Littleproud told ABC radio.