A chilli crop in Western Australia's Gascoyne food bowl region is set to be destroyed, after it was found to be riddled with Mediterranean fruit fly (Medfly).

Work is underway across the horticultural town of Carnarvon to eradicate Medfly, through use of trapping and baiting, with plans to release millions of sterile male fruit flies next year.

This particular infestation was found after nearby Medfly traps recorded more than 500 insects per week.

Local Department of Agriculture and Food biosecurity officer, Sandy Leighton, said the growers at the affected plantation were keen to manage the outbreak and prevent any reoccurrence.

"We had a meeting face to face with the two growers and they really wanted our help," she said.

"They're going to destroy their crop, which is a fantastic outcome for us.

"They have another, younger crop at the back of the plantation and they've also asked for some help with that."

Ms Leighton said Medfly management at the plantation would require the use of insecticide.

"We've dissected the fruits and the red, very ripe, chillies are the ones that the Medflies seem to love," she said.

"We were getting up to five or six larvae per chilli.

"The main information we're trying to convey to the growers is one, to use the most appropriate insecticide, and two, to make sure they adhere to the withholding period (of seven days) before picking again.

"So it'll be a little bit complex but we're committed to working with them."

Good plantation hygiene is the best way to prevent the spread of Medfly, according to Ms Leighton.

She said there may be opportunities to work with third-party companies in the future to help protect against Medfly.

"Some of the citrus growers are doing an excellent job at clearing up underneath their trees and this coming mango season we're hoping to work with some of the larger growers too," she said.

"One of the ideas we're pursuing is talking with a company that wants to grow sugarcane and wants to access disposed fruit to make compost.

"Growers could dump into a container and, in an ideal world, we would work with this company, who would collect the fruit and use it in hot compost, which would kill off the Medfly larvae."

While that possible collaboration is still in its very early stages, Ms Leighton said she hoped to flesh out the future opportunities for growers' spoiled fruit next month.