"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.