The peak body representing commercial fisheries in Victoria says it is a "black day" for the industry, after legislation was passed banning commercial net fishing in Port Phillip and Corio Bays.

The ban will be implemented over the next eight years and the 43 commercial fishing licence holders will share in compensation worth $27 million.

Commercial net fishing accounts for a small portion of the annual catch from Port Phillip Bay - about 700 tonnes.

Recreational fishers are estimated to have caught almost as much in snapper alone over the past year.

Leading Melbourne chefs, wholesale seafood suppliers, retailers and commercial fishers gathered on the steps of State Parliament on Monday to present a petition against the bill to Greens MP Greg Barber.

Agriculture Minister Jaala Pulford said it was a historic reform that people had been calling for since 1971.

"I think that the arrangements Parliament agreed to will pave the pave the way for a quick exit and a quick improvement to recreational fishing in the bay," she said.

Seafood Industry Victoria executive director, Johnathon Davey, said the industry had been third-party assessed as sustainable and passage of the bill was "gut wrenching".

He said the compensation on offer was "minimal".

"[It's] no way near enough to go and invest in another fishery," he said.

"Most of these families are fourth and fifth generation fishing families. Fishing is all that they know, fishing is all that they want to do."

The Minister acknowledged it would be a difficult transition for the families involved.

"It's a really, really dark day for the Victorian seafood industry," Mr Davey said.

The Government's Target One Million strategy for recreational fishing aims to increase the number of anglers from around 750,000 to one million while phasing out net fishing over eight years.