Wild fish stocks in Australian waters shrank by about a third in the decade to 2015, declining in all regions except strictly protected marine zones, according to data collected by scientists and public divers.

The research, based on underwater reef monitoring at 533 sites around the nation and published in the Aquatic Conservation journal, claims to be the first large-scale independent survey of fisheries. It found declining numbers tracked the drop in total reported catch for 213 Australian fisheries for the 1992-2014 period.

The biomass of larger fish fell 36 per cent on fished reefs during 2005-15 and dropped 18 per cent in marine park zones allowing limited fishing, the researchers said. There was a small increase in targeted fish species in zones that barred fishing altogether.

"Most of the numbers are pretty shocking," said David Booth, a marine ecologist at the University of Technology Sydney. “This paper really nails down the fact that fishing or the removal of large fish is one of the causes” of their decline.

Over-fished stocks include the eastern jackass morwong, eastern gemfish, greenlip abalone, school shark, warehou and the grey nurse shark. The morwong catch, once as common as flathead in the trawl fishery, dived about 95 per cent from the 1960s to 109 tonnes in the 2015-16 year to become basically a bycatch species.