A tiny fruit fly is undermining Australia's efforts to grow its $4 billion fruit and vegetable exports, despite the country reaching a series of free trade agreements with its largest trading partners in Asia.

Australia sealed trade agreements with China, Japan and Korea last year - deals that guaranteed a significant reduction in tariffs for agriculture produce - and were heralded as a catalyst for rapid expansion in exports.

The Queensland fruit fly is causing headaches for would-be fruit exporters. Pic of Queensland fruit fly supplied by DPI victoria ...

The tariff cuts have pushed sales of agriculture produce to all-time highs, but difficulty obtaining biosecurity permits - so called phytosanitary protocol agreements - means many fruits in particular cannot be sold into markets like China, making free trade agreements often meaningless, industry executives say.

"Phytosanitary protocol agreements are the biggest hurdle we have to overcome to get our products into markets like China," said Annie Farrow, Industry services manager at the industry body, Apple and Pear Australia.