Development along the Great Barrier Reef must have a "net benefit" to the condition of the reef under a plan released on Friday.
Federal Environment Minister Greg Hunt and his Queensland counterpart Andrew Powell released the Great Barrier Reef strategic assessment in Townsville.
The report came after UNESCO last year raised concerns about the health of the World Heritage-listed marine park area, which extends more than 2300km along the Queensland coast and covers 346,000 sq km.
The international agency warned coastal development needed better controls or the reef could be listed as "in danger".
The strategic assessment concluded the best way to halt and reverse damage to the reef was to put in place a new management framework and examine the "cumulative effect of human activities and natural forces", rather than impacts in isolation.
It also called for a "net benefit policy", so that any activities along the coast and in the marine park produced an overall benefit to the condition of the reef.
"Everyone wants to see the reef remain one of the most biologically diverse places on the planet so it can be enjoyed by future generations," Mr Hunt said.
"Having long-term actions and partnerships in place for tackling the challenges facing the reef helps to provide greater certainty for the community, industry and the environment."
The report found much of the damage to inshore reefs was due to the crown of thorns starfish, which benefited from run-off of sediments and pesticides.
It said a new reef recovery program was needed, involving local communities, industry and indigenous groups, as well as a reef-wide monitoring and reporting program.
The strategic assessment will be open for public comment until January 31.
Australian Marine Conservation Society reef campaign spokeswoman Felicity Wishart welcomed the assessment but said the federal and state governments should halt development along the Queensland coast if they're serious about protecting the reef.
"If the target is to improve the health of the reef then stop doing anything that's going to be damaging it," she told AAP.
"I have no doubt that there has been some very hard work done into this by some very dedicated people from GBRMPA.
"But the best science in the world won't protect the reef if the management arrangements ignore the science."
Of most concern to environmentalists is the planned expansion of Abbot Point coal port, near Bowen, which would involve dredging three million tonnes of soil to allow ships to access the terminals.
The port authority, North Queensland Bulk Ports, plans to dump the soil within the World Heritage area.
Mr Hunt is due to decide next month whether to give the project the green light.
Ms Wishart says if the government really wants to improve water quality then it should reject the proposal because it will hurt marine life and turn the reef into a shipping super-highway.
North Queensland Bulk Ports has said sediment could damage seagrass but would have little impact on other flora and fauna.