Climate change and water pollution were acting as a “double whammy” on the reef’s health, said the report compiled by natural resource management groups.
The report called for co-operation from farmers and rigorous coastal planning.
The reef, a major tourist destination and a rich marine habitat, faces many threats to its eco-system.
Rising sea temperatures and pollution from agriculture are believed to be among the biggest dangers.
Among other threats, the latest report highlighted the destruction of coral by outbreaks of Crown of Thorns starfish, which were caused by nitrogen run-offs from farms.
The Reef Regions Investment Plan, prepared by six natural resource management groups operating in the state of Queensland, found that floodplains, their wetlands, and estuaries and their habitats were the most degraded parts of the reef’s eco-system.
“Managing, repairing and protecting the reef is not a start-stop-restart activity,” said the authors of the report.
They called for secure investment, as well as five-yearly progress reviews and the “readjustment of priorities and investment profile in the context of review findings”.
The report also reviewed the Australian government’s plan to protect the reef, the Reef 2050 Long-Term Sustainability Plan.
It suggested that many of the targets in the plan are ambitious, especially without further investment.
The reef’s environment is expected to come under further strain with the proposed expansion of ports to export coal.