Fishing groups say the Queensland Government's new plan for Moreton Bay will cost the industry more than $60 million.
From March next year, 16 per cent of Moreton Bay will be protected from fishing and more "go slow" areas will be introduced to protect dugongs from boat strikes.
Premier Anna Bligh says the "green zones" will help protect fish populations for the future.
"Without this protection Moreton Bay could have been the one that got away," Ms Bligh said.
Ms Bligh says the 750 fish species, as well as dugongs and dolphins that live there needed more protection.
"Protecting these areas is critical to ensuring that we have species biodiversity for the future," she said.
But the Liberal National Party (LNP) says the State Government did not use enough scientific evidence when it developed its new zone plan.
Opposition agriculture spokesman Ray Hopper says the zone plan will upset the commercial fishers.
"Whether 16 per cent is enough or too much, we are yet to look at the details of this whole deal," he said.
"Of course there's the $15 million package for a buy back of licences - I've got to meet with these guys and see if they're happy with that and we've got to get across this whole issue and find out the exact detail."
Business 'ignored'
Queensland Seafood Industry Association (QSIA) spokesman Martin Hicks says the Government has listened to environmental lobby groups but has ignored business.
He says the Government's $15 million compensation package will not cover the huge losses the industry is now facing.
"A lot of the area will be closed down, which will make their whole fishing operation unviable," he said.
Mr Hicks says the environmental benefits will be small because most of the fish in Moreton Bay are migratory and will not stay in the green zones.
But Australian Marine Conservation Society (AMCS) spokesman Craig Bohm says the ban does not go far enough.
"It exposes actually a whopping 84 per cent of the marine park to intense fishing pressure," he said.
He says they wanted at least 30 per cent of the bay protected.
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