Two outbreaks of an exotic insect pose a major threat to Queensland's $360 million cotton industry.

Biosecurity Queensland has confirmed an exotic species of mealybug is affecting cotton crops in Emerald, in central Queensland, and cotton farms in the Burdekin region, in the state's north, for the first time.

There are many species of mealybugs - small, sucking insects found on a range of plants - but the type of mealybug recently found in Emerald and the Burdekin are native to North America and have been known to cause major crop losses for overseas cotton farmers with recent cases reported in India and Pakistan.

Authorities are yet to trace how the insects arrived in Queensland.

Biosecurity Queensland general manager Mark Panitz says the priority is to protect Queensland's cotton industry.

"The biggest priority at this point is to try and limit further spread of the mealybug from and within Emerald and Burdekin cotton production areas," Mr Panitz said.

"As harvesting of crops in Emerald will soon begin, we are working with the cotton industry to develop wash-down and decontamination protocols for harvesting machinery."

Mr Panitz said the cotton industry was discussing long-term crop and fallow management options.

He said the outbreaks won't stop the harvest in Emerald or the Burdekin.

Mealybug hallmarks include crinkled and twisted leaves, fewer flowers, reduced and smaller bolls, and distorted and stunted plants.