Australia admitted Wednesday conditions at the Great Barrier Reef are "poor" as it battles UNESCO threats to downgrade its heritage status over concerns about pollution and development.
Environment Minister Mark Butler released a report card showing that the reef's health had slumped since 2009 due to cyclones and floods, despite progress on reducing agricultural runoff.
"Extreme weather events significantly impacted the overall condition of the marine environment which declined from moderate to poor overall,' the report said.
It said key reef ecosystems were showing "declining trends in condition due to continuing poor water quality, cumulative impacts of climate change and increasing frequency and intensity of extreme events".
Despite reductions in nitrogen (seven percent), pesticides (15 percent), sediment (six percent) and pollutants key to outbreaks of devastating crown-of-thorns starfish (13 percent), the report said the reef was in trouble.
Major flooding in 2010-2011 followed by powerful cyclone Yasi had badly damaged the world's largest coral reef, degrading water quality and depleting overall cover by 15 percent.
"Full recovery will take decades," the report said.
Conservationists said the report was alarming and showed the need for far greater action from the government, with the current plan and targets "unlikely to save our reef".
"The outlook for the reef is not good but the situation isn't hopeless, solutions do exist," said WWF's Nick Heath.
"We just need more investment, more targeted action in the most dangerous pollution hotspots."
While reductions had been achieved, Heath said they were far short of 2009 targets, particularly pollutants key to starfish outbreaks, which fell by 13 percent instead of 50 percent -- a goal now pushed back to 2018.
"We are likely to need a nitrogen pollution reduction target of up to 80 percent if we are to arrest crown-of-thorns outbreaks," he said.
A major longitudinal study of the reef's health, published last year, revealed that coral cover had more than halved due to storms, predatory starfish outbreaks and bleaching linked to climate change over the past 27 years.
Intense tropical cyclones were responsible for much of the damage, accounting for 48 percent, with the coral-feeding starfish linked to 42 percent, according to the study.
UNESCO has threatened to downgrade the reef's world heritage status to declare it at-risk in 2014 without significant action on rampant coastal and resources development seen as a threat to its survival.
Scientists who advised the government on the reef's health for the report card said declining water quality associated with agricultural and other runoff was a "major cause of the current poor state".
The team, led by James Cook University's Jon Brodie, said intense floods and cyclones had also "severely impacted marine water quality and Great Barrier Reef ecosystems".
"Climate change is predicted to increase the intensity of extreme weather events," it said.
Butler unveiled lofty targets for improving water quality over the next five years, aiming for at least a 50 percent reduction on 2009 levels of nitrogen pollutants linked to crown-of-thorns starfish outbreaks, 20 percent for sediment runoff and 60 percent for pesticides.
"In spite of solid improvement, data tells us that poor water quality is continuing to have a detrimental effect on reef health," Butler said.
"To secure the resilience of the Great Barrier Reef it is critical that we build on the momentum of the previous reef plan with a focus on improving water quality and land management practices through ambitious but achievable targets.