The Great Barrier Reef Marine Park Authority report on the status of the reef said turtle and dugong (a marine mammal) populations had dropped dramatically, the worst ever coral bleaching episodes occurred in the past five years and fishing was increasing.
"We are seeing continuing decline in the state of the reef," said Environment Minister David Kemp, adding that the report made sobering reading.
The report, unveiled at a conference here Friday, found the annual flow of land-based pollutants has increased fourfold since European settlement.
Nesting loggerhead turtles had declined by 50-80 percent in 40 years and dugong numbers were three percent of what they were in the early 1960s.
Recreational fishing was increasing and the reef line fishery has doubled since 1995.
The reef had suffered its two worst ever recorded coral bleaching events in the past five years, possibly due to global warming, the report said.
Kemp said the government was taking action, such as its push to increase areas of the reef closed to fishing from five to more than 30 percent.
"The great positive is that the Great Barrier Reef is not only the world's largest coral reef but it's probably also the world's healthiest large reef," he said.
"It is the responsibility of this community that where there is good scientific evidence of this decline, we act to put the reef on a healthy basis in future."
But opposition Labor environment spokesman Kelvin Thomson said the government needed to ratify the Kyoto Protocol on global warming and act urgently to implement pollution targets.
"It needs to set targets to control sediments, control phosphorous, control nitrogen," he said. "It needs to ratify the Kyoto protocol on climate change, it needs to protect the reef from threats posed by shipping."
Dugong expert Helene Marsh said the animal, which is believed to have inspired the mermaid myth, was falling victim to shark nets, boats and high levels of indigenous hunting.
In the Torres Strait, about 1,000 dugong were hunted each year but the region's population could only sustain the loss of 154 at most, she said.
Marsh called for go-slow zones for boats, more regulation of hunting and more resources for indigenous communities to police regulations.
Acclaimed US marine biologist Sylvia Earle warned only National Park-style no-take areas on the world's reefs could protect wild fish stocks. "If you keep going the way we are now, there is little hope there will be a commercial fishing industry in the future," she said.