Professor Lester said Argentine ants were known to raid beehives and also forage in the same environment as honey bees.
"Such close contact is bad for bees, as their association likely promotes pathogen exchange."
The finding came after Professor Lester, along with a team that included Victoria University researchers and a team of ESR scientists known as The Virus Hunters, began investigating why some populations of the ants were faring better than others.
"One reason for that was the possibility of pathogens - so the starting point for our study was to do some genomic work to determine if these invasive ants do carry viruses."
As well as the deformed wing virus, the group found and have described a virus new to science. So far it has only been found in these ants.
While the detection of the viruses adds a new dimension to concerns around invasive species, just how much the ants might be contributing to bee colony loss remained to be seen.
"But it's really interesting to us that there are viral pathogens that are really widespread, quite abundant and replicating in, or parasitising, ant populations."
"This virus hasn't been seen before, but it's related to other viruses that can devastate populations of other insect species," Professor Lester said.
"If the virus is host-specific and managed correctly it could be used as a biopesticide both in New Zealand and overseas."
The university's commercialisation office, Viclink, was now supporting work to develop the finding into a marketable product.
"This is an exciting opportunity to develop a naturally-derived species-specific insecticide that could reduce reliance on chemical products, which often indiscriminately kill all insects," Viclink senior commercialisation manager Jeremy Jones said.
"It could be a game-changer for our fruit and wine industries where controlling this ant is a growing problem."
Argentine Ants
• Worker ants of the species measure between 2-3 mm long and are a uniform honey-brown colour.
• Listed by the World Conservation Union as one of the world's worst invasive species.
• Originally established in Auckland in 1990, and now a problem in an increasing number of towns and cities throughout New Zealand.
• Spread through different areas by hitching rides in freight, potted plants, rubbish, vehicles and other such goods.
Source: Landcare Research