This is significant, signalling a process of implacable decline. The reef may still be magnificent for much of its 2000-kilometre length but the long-term trend is clear and ominous. It takes a long time for something so large and complex to be reduced to a remnant, but that is what is happening. During the past three decades, the reef has shrunk to half the size it was about a century ago. Vast tracts of coral have died.

The threats are growing, not diminishing. Even setting aside the challenges caused by a rise in the world's atmospheric and ocean temperatures, the reef will have to cope with the impact of an industrialisation along the Queensland coast that is unprecedented in scale. More than 40 big projects - ports, coalmines, liquid natural gas plants, railway lines - are being developed in one of the biggest infrastructure projects in Australian history.

The Newman government in Queensland has moved to streamline the planning process as part of its commitment to making development easier. Queensland governments have traditionally been extremely territorial about reef policy, which means they own the offshore consequences of coastal development, land clearing and farming.

Now comes the disheartening news, via the latest reef health report, that even destructive forces that can be contained are not being contained. In 2009, the then federal minister for the environment, Peter Garrett, extracted $200 million from the federal budget for a reef rescue plan to fund changes to land management practices on farms, industry and resorts. The main target was sugar farms and the main goal to halve chemical and fertiliser run-off in four years. Four years later, the target is not even close to being met.

Since then, the science has become incontrovertible that what have been causing the plagues of crown of thorns starfish - the single most damaging agent of coral destruction - are the plumes of nutrients flowing into the ocean in the run-off from farming and development.

When the amount of plant and nutrient content in water doubles, the survival rate of the crown of thorns larvae increases exponentially. The reef rescue program is thus critical - but efforts to reduce polluted run-off were hampered by extensive flooding and cyclone Yasi in 2011.

Even more disheartening is the assessment that much of the damage to the reef is caused by elements beyond Australia's ability to control, notably coral bleaching, higher water acidity and cyclones.

Coral bleaching is caused by higher water temperatures. Higher water acidity is caused by increased levels of carbon dioxide absorbed in the ocean. Both higher water temperature and increased acidity can be attributed to a warming of the atmosphere. Cyclones have always been prevalent in tropical Queensland. No matter what policies the federal and state governments introduce, Australia will have little impact on these global forces.

But where governments can mobilise is in slashing the water pollution from farms and other developments on the coast. The new federal Minister for the Environment, Mark Butler, has announced a further $375 million will be spent during the next five years to reduce run-off from farms and to improve coastal water quality.

But the federal government can do only so much. The reef needs a strategic management plan that co-ordinates the state and federal agencies' response to run-off reduction, infrastructure projects, ports and shipping lanes. They are all connected and need to be treated as such if the next reef health report is not be as disturbing as the one released this week. As a nation we must make a national priority to remove the reef's crown of thorns.