The Great Barrier Reef.

"The health of the Great Barrier Reef has gone down very dramatically,": Senior scientist Hugh Sweatman is not suprised at the downgrading of one of Australia's natural wonders. Photo: Simon O'Dwyer

The health of the World Heritage-listed Great Barrier Reef has been downgraded to "poor" as the government quietly pushed some of the pollution targets that were supposed to be achieved this year back five years.

In 2009, former environment minister Peter Garrett approved a plan to cut the chemical and fertiliser runoff that is poisoning the reef by a minimum of 50 per cent by this year – a level then seen as essential for saving the reef. But the fresh plan, announced by new environment minister Mark Butler on Wednesday in a bid to avoid having the reef's World Heritage status downgraded, shifts some of the targets back to 2018.

Mr Butler cited changes in research methods, and also blamed the Queensland floods and Cyclone Yasi for damaging the reef. "This and changes in our understanding of management practice impacts on water quality have necessitated some variation in the targets set under the Reef Plan, but we continue to work hard, in difficult circumstances, to meet our targets,” he said.

Some of the pollution targets were still within reach this year, the government stressed. Pesticide runoff could yet be halved by the end of this year, he said.

After a meeting of federal and state environment ministers on Wednesday, Mr Butler announced that $375 million would be spent between 2013 and 2018 to reduce run-off from farms and improve overall water quality.

The new plan is the central part of the government's effort to stop the reef being listed as a "World Heritage Site In Danger". The UN body UNESCO will deliver its verdict on the reef's health next June, but it has already voiced concerns about the impact of major oil and gas developments planned for the Queensland coast.

The reef health report card, released on Wednesday, painted a grim picture of decline, and downgraded the reef's overall status from "moderate" to "poor".

A panel of leading marine scientists, representing major universities and research institutes, agreed with the poor health score card.

"The overarching consensus is that key Great Barrier Reef ecosystems are showing declining trends in condition due to continuing poor water quality, cumulative impacts of climate change and increasing intensity of extreme events," the scientists' statement said.

There was some progress in addressing polluted runoff onto the reef. Nitrogen was reduced by 7 per cent between 2009 and 2011, as farmers were encouraged to change land management practices, and sediment dropped 6 per cent.

Last year a landmark scientific study reported that half of the reef's coral had disappeared in the past 27 years and could halve again in the next decade unless action was taken to halt the decline. The report by scientists at Townsville's Australian Institute of Marine Science found coral had been wiped out by intense cyclones, coral bleaching and a native species of starfish, crown of thorns, which thrived in waters rich in nutrient runoff from agricultural land.

"Coral cover is the simplest index of reef health, and the health of the Great Barrier Reef has gone down very dramatically," said a senior scientist at AIMS and co-author of the study, Hugh Sweatman.

The research team said parts of the reef could recover if crown of thorn populations were controlled by improving water quality and developing other methods of control.