Fifteen research positions have been axed at Queenscliff's Marine and Freshwater Discovery Centre.
In State Parliament yesterday, Bellarine MLA Lisa Neville called on Agriculture Minister Peter Walsh to explain the cuts.
"The impact of these savage cuts, slashing the current number of positions in half from 30 to 15, will have a disastrous impact on our local fishing industry and marine environment," Ms Neville said.
She said it was staff at the centre who developed a hatchery to produce a reliable high quality spat (baby mussel) that was vital for the mussel industry.
"This is the sort of innovative, world-class research and development work that has been achieved at the Queenscliff centre," she said.
"The potential for developments of this calibre in the future is at serious risk with cuts of this magnitude to the research capacity."
Ms Neville also said the cuts would undermine the work done with schools and universities, and with families and visitors to the centre on the shores of Swan Bay.
"These educational and interactive programs promote an understanding of the complexity and importance of our marine environment," she said.
Ms Neville said the loss of so many positions would weaken the future of the fisheries industry and the protection of the ocean.