The fungus Monosporascus cannonballus, which causes root rot in cucurbit plants such as pumpkins, squash, melons, cucumbers and gourds, was confirmed in August after two farmers noticed something wrong with their crops.
Northern Territory Chief Plant Health Officer Sally Heaton said the disease was detected in a cucumber plant in the Darwin region and in honeydew and rock melon crops in the Katherine region, about 300 kilometres to the south.
Dr Heaton said the fungus could not be eradicated, and that if left unmanaged, growers overseas had seen whole mature crops suddenly die off.
"Once you've got it into your crop, you really can't do much to save it," she said.
The disease, which causes plants to look as though cannonballs are erupting out of their roots, has spread in multiple countries including the US, India, Taiwan, Japan and parts of Europe and the Middle East. Dr Heaton said authorities were not sure how the disease arrived in Australia, but it could have been present for a long time.
Melons Australia chief executive Johnathon Davey said the discovery was concerning and was causing "significant loss" for affected NT growers, who were already grappling with other challenges including varroa mite.
"We now need to really work with our growers to understand what the spread of this fungus is and start working with them on how to manage it," he said.
Mr Davey said the incursion would likely lead to increased production costs and higher prices for consumers.
"Providing fresh melons for Australian consumers is only [going to] become harder," he said. "This is going to see increased management costs."
He said that if it became clearer how the disease entered the country, a "fairly substantial investigation" could be expected.
NT authorities are not planning to impose biosecurity restrictions in response to the detections.