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".
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 per cent.
"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.
While reductions had been achieved, Heath said they were far short of 2009 targets, particularly pollutants key to starfish outbreaks, which fell by 13 per cent instead of 50 per cent -- a goal now pushed back to 2018.
"We are likely to need a nitrogen pollution reduction target of up to 80 per cent 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.
UNESCO has threatened to downgrade the reef's world heritage status to declare it at-risk in 2014.
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