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The Reef Water Quality Protection Plan, released yesterday by the Queensland and federal governments, also found farmers had greatly improved runoff control in the past decade.

The report found that of the loss of coral cover in the past 27 years, 48 per cent was caused by storm damage, 42 per cent by crown-of-thorns starfish, and 10 per cent by bleaching, primarily linked to climate change.

The reef has been badly hit by storms in recent years, particularly Cyclone Yasi in 2011 and Cyclone Larry in 2007. The main reason for the spread of the crown-of-thorns is that fertiliser used by farmers runs off into the water system and flows to the reef where it fertilises algae, the main food source of baby crown-of-thorns. The resulting adult starfish then eat coral.

The report found seagrass on the reef was in very poor condition overall, as were inshore coral reefs.

A scientific consensus statement accompanying the plan found that the coral cover in the northern part of the Great Barrier Reef -- lying mostly off Cape York -- "has not shown the consistent downward trend seen along the developed coast of the central and Southern Great Barrier Reef".

The report notes this is largely because there is hardly any agricultural activity on land beside this part of the reef, while conversely, the area where coral cover has been most affected, the central and southern reef, is where most of the sugar industry in particular is situated.

The scientific consensus found "that reef ecosystems are showing declining trends in condition due to poor water quality, cumulative impacts of climate change and increasing intensity of extreme weather events".

The report also found that farmers had become far better at targeting the use of fertilisers and pesticides on their crops. Nitrogen levels, mainly from fertiliser runoff, had dropped by 7 per cent, pesticides by 15 per cent, and dissolved nitrogen by 13 per cent. Dissolved nitrogen, when fertiliser is broken down and exists in water, is "the key pollutant of concern due to its influence on crown-of-thorns starfish outbreaks".

State and federal governments used the occasion of the release to announce initiatives to protect the reef. The federal government said it would invest $200 million and the Queensland government announced $175m for reef protection programs, all aimed at reducing chemical runoff.

Federal Environment Minister Mark Butler said "in spite of solid improvement, data tells us that poor water quality is continuing to have a detrimental effect on reef health".

World Wildlife Fund Great Barrier Reef program leader Nick Heath said the outlook for the reef was not good but neither was it hopeless. "We just need more investment, more targeted action in the most dangerous pollution hotspots," he said.

He criticised the postponement of the target of 50 per cent nitrogen pollution reduction from 2013 to 2018, and said a target of 80 per cent reduction was more realistic to arrest crown-of-thorns outbreaks.