It is hoped the sterile flies will mate with wild fruit flies, stopping the breeding cycle and wiping out any remaining population.

The flies were released across inner-city suburbs including Moonee Ponds, Flemington and Kensington as part of the final steps to eradicate an outbreak that occurred in December 2007.

The outbreak, near the Melbourne Wholesale Fruit and Vegetable Market, jeopardised Victorian fruit exports.

Agriculture Minister Joe Helper said the sterile flies had been used before in Victoria and overseas as a way of controlling the pest.

"It's a terrific way of overwhelming the fruit fly population with sterile fruit flies so that their life cycle comes to an end as soon as possible."

Mr Helper said it was important that the Government get on top of inner-city outbreaks, because the effect of contamination on the market would be felt around the state.

"Any fruit that moves through an affected area has to be properly treated, has to be appropriately packaged and has to be certified. That is a cost," he said.

Mr Helper said that although the 2007 outbreak was well under control, it was important that residents in affected areas continued to be on the lookout.

"We want people to be extremely careful in terms of transferring fruit and we want people to be very vigilant in their backyards," he said.