Excessive fishing has caused stocks of large Australian fish, like bream and snapper, to decline by a third according to new research which has been called a "wake up call" for Australia.

But the authority which manages the nation's fisheries has slammed the research as flawed.

The 10-year study, looking at nearly 200 species at 544 sites, found the main cause for decline was overfishing, but climate change has also contributed.

It compared areas where fishing was allowed to marine park areas where there was either limited fishing or no-take zones, and concluded that on fished reefs, the number of large fish declined by 36 per cent.

This was compared to 18 per cent in zones where there was limited fishing. In no-take zones, stocks remained stable.

The study's authors said there was an urgent need for more protection zones for fish. ( ABC News: Supplied )

Marine scientist Trevor Ward said there was an "urgent need" to declare more marine reserves.

"Effective marine management is needed now, more critically than ever," the researchers said.

"Despite public desire for marine protected areas … [they] cover less than 2 per cent of global marine waters."

A single marine reserve can provide insurance against population decline for hundreds of species if well designed, the study by the University of Tasmania and UTS said.

The call for more protection was backed by marine scientist Professor David Booth, who said the study was "a real wake-up call for our nation".

However, the paper, published in Aquatic Conservation, has been heavily criticised by the Australian Fisheries Management Authority, which has labelled the claims baseless.

No fishery solely managed by the Commonwealth has been subject to overfishing in the last four years, the Fisheries Authority says. ( ABC News: Supplied )

"The premise of the paper that there has been a general decline in Commonwealth fisheries is not supported by the weight of evidence," AFMA's acting CEO Nick Rayns said in a statement.

"Current Commonwealth fisheries management is based on a range of new measures brought in since 2006-2007, the year after the baseline year of 2005 used frequently in the paper," Dr Rayns said.

Dr Rayns also questioned the way scientists reached their conclusions.

"The paper uses commercial catch as a proxy for biomass when there are many reasons which catches may rise or fall over time," he said.

But Professor Ward said the research aimed to find more efficient and effective ways to increase fish stocks and it was intended to help, rather than criticise Australian Fisheries management.

"Well-designed marine reserves will lead to more fish for everybody to catch in the years and decades to come," he said.

