Environment Minister Tony Burke says Australians should be alarmed by a halving in the coral cover in the Great Barrier Reef since 1985.
A report from the Australian Institute for Marine Science (AISM) released on Tuesday said total coral cover in the reef dropped from 28 per cent in 1985 to 13.8 per cent 27 years later.
"I reckon today's report would have sent shockwaves through a whole lot of households," Mr Burke told ABC Television on Tuesday.
"We have all heard about damage to the reef over the years, but that 50 per cent figure rang a warning bell loud and clear for many people."
The AISM figures are based on analysis of 2258 surveys of 214 individual reefs between 1985 and 2012.
Researchers say cyclones are responsible for 48 per cent of the loss, while crown of thorns starfish accounted for 42 per cent and coral bleaching the remaining 10 per cent.
The study says lowering the number of starfish could improve the reef's outlook, but only if climatic conditions are stabilised.
Mr Burke says reducing the starfish is by a two-pronged attack.
One is by killing the starfish directly and the other is to reduce the impact of runoff from land, he said.
"The crown of thorns (starfish) are native, we need to have some of them," Mr Burke said.
"The problem is you get a massive increase in the numbers when you get too much in the way of nutrients and runoff coming down from the reef."
He says programs begun five years ago should have started 20 years earlier to improve the health of the marine park.
"A number of things that this report calls on us to do we are doing, but there's no doubt that there has been a level of neglect for decades, which if it had been dealt with otherwise, we'd be in a much better situation now," Mr Burke said.
The minister says the government had provided $200 million for the reef rescue program.
"In five years I am not going to pretend that $200 million has turned the corner on every single property, but it is making a very significant difference," Mr Burke said.