Port Phillip Bay's once struggling mussel industry has its sight set on nearing a full recovery within two years.

Port Phillip Bay's once struggling mussel industry has its sight set on nearing a full recovery within two years.

In Queenscliff as part of Community Cabinet, Minister Responsible for Fisheries Joe Helper said the industry was going from strength to strength thanks to a successful collaborative research program between Government and industry.

"Without the collaborative investment, the bay's mussel farming industry would probably be non-viable by now," Mr Helper said.

"So it was vital the Brumby Labor Government took immediate action to work together with industry and its great to see that this year's harvest will produce around 500 tonne of mussels. "In even better news that figure is expected to double next year."

Funded jointly by the Brumby Government's $205 million Future Farming Strategy and industry, the program involved the development of a small state-of-the-art bivalve shellfish hatchery and a production and selective breeding research program.

Mr Helper said before the hatchery was established, Victorian mussel harvest had fallen dramatically because of poor availability of wild spat (baby mussels) in Port Phillip Bay.

"The shortage of spat is thought to be due to the impacts of drought, exotic marine species and other environmental factors," he said.

"A joint research and development agreement was developed between Government and industry to start a hatchery-based mussel breeding program at the Department of Primary Industries' Queenscliff research facility to address the shortage.

"After some teething problems were sorted out, the research collaborators in partnership with mussel industry employees successfully produced spat at the Queenscliff hatchery this year and are now looking at ways to utilise new technology to expand what the hatchery can produce."

Mussel farmer Lance Wiffen said the industry would recover to its previous level within two years. "It's fantastic to finally see a big bright light at the end of a long tunnel," Mr Wiffen said.

Member for Bellarine Lisa Neville said it was fantastic to see the bright outlook from an industry that had been doing it tough.

"Aquaculture is such an important part of the Bellarine region and the mussel industry has faced some bleak times," Ms Neville said.

"However through industry working with the Brumby Labor Government, the horizon is much brighter which can only be a good thing for the Bellarine."