The carp herpesvirus is set to be released into Australian waterways in 2018, but Canberra fish hobbyists are concerned about the impact on ornamental species.
Keeping ornamental koi carp is a popular hobby in the ACT, NSW and WA - the only states and territories in Australia where it's legal to own the pest species.
The virus is a particularly virulent strain which is said to only affect the noxious fish and is spread through contact or infected water.
It will be introduced by the federal government in a $15 million plan to rid waterways of the pest.
Jem Aquatics Belconnen manager Melissa Gray, who sells the colourful breed of carp, said her main concern wasn't for the retail stock but for the people who keep their fish in outdoor ponds.
"I do worry about customers and what effect it would have on them," Ms Gray said.
"I would like to [see a vaccine introduced]. There are a lot of people who keep koi in ponds in Canberra, and not just personal ponds but there are a few bigger public ponds that have them and I'd hate to see the effect on those."
Queanbeyan Reptiles Inc and Aquarium part-owner Antony Pezzella said koi were popular in the region because they were outdoor fish which could survive the harsh conditions.
He said prized show koi were worth "an absolute fortune", but the sentimental value for the fish was often higher.
NSW Department of Primary Industries has ruled out introducing a vaccine for pet fish. A spokesperson said the vaccine would reduce the effectiveness of the virus as a biocontrol agent if wild carp were exposed to it.
"In the past industry members opposed to the release of a biocontrol agent have requested the government make a vaccine available," the spokesperson said, citing the example of rabbit owners when the calicivirus was introduced.
"It is possible the ornamental koi industry could make a similar request."
But investigations into the practices employed by koi breeders overseas had shown biosecurity measures could be highly effective in protecting the captive populations, the spokesperson said.
"The government intends to provide educational campaigns to assist ornamental koi industry members to improve their biosecurity measures."
According to the CSIRO, which has been researching the virus for seven years, koi fish are "completely susceptible" and biosecurity measures for purpose-bred fish would certainly need to be taken.