Commercial fishers say the net effect of Australia's new marine sanctuaries on the global environment will be negative because it will put pressure on Asian fisheries.
The National Seafood Industry Alliance had scrutinised the federal government's regulatory impact assessment for the sanctuaries and concluded the process was inadequate, West Australian Fishing Industry Council chief executive Mark Tucek said.
The alliance wrote to federal Environment Minister Tony Burke outlining its concerns, but had not yet received a response, he said.
"There are serious gaps in the regulatory impact statement," Mr Tucek told AAP.
He said Australia imported about 75 per cent of its seafood for human consumption from countries such as China, Vietnam and Thailand, where ecosystems were under great stress and fisheries were not as professionally managed.
"It exports an increase in our demand to those countries and puts more pressure on their environmental systems," he said.
"The environment doesn't stop at Australia's economic exclusion zone, so the net effect to the environment is negative."
Mr Tucek said many coastal communities were dependant on the livelihood of commercial fishers and that had not been accounted for in the federal government's $100 million per annum compensation to the industry.
Similarly, Recfishwest said businesses which relied on recreational fishing, including charter operators and holiday accommodation suppliers, would be hard hit.
But the Conservation Council of Western Australia said the sanctuaries would open the door to greater scientific discoveries and breakthroughs as there was still much to understand about Australia's oceans, where up to 80 per cent of marine life was yet to be named.
Australian Greens Senator Rachel Siewert said the party wanted to see the sanctuaries "in place in perpetuity".
Protecting the highly biodiverse waters of the South West region, for instance, and protecting the fishing industry were not mutually exclusive goals, Ms Siewart said.
"They go hand in hand," she said.