A national survey of Australia's fishing habits has raised the possibility that some Indigenous communities may consider capping the take of dugongs and turtles.

Federal Fisheries Minister Ian Macdonald released the survey - the first of its kind - in Sydney today.

The survey found thousands of fish and sea creatures listed as protected were killed through Indigenous fishing over a year.

Senator Macdonald says 44 communities from Broom to Cairns were monitored over a 12-month period.

The Torres Strait was not included in the survey.

Senator Macdonald says some of the species included dugongs and turtles.

He says while the catch was legal the numbers highlight the need for more sustainable fishing in Aboriginal communities.

He says that while the Aboriginal community only represents 2 per cent of the population, some 92 per cent of Indigenous people fish.

Senator Macdonald says while endangered species such as the dugong have been sustainably harvested by Indigenous people over many thousands of years, there's concern things may have changed.