The overall health of the Great Barrier Reef is still poor, but Environment Minister Greg Hunt says the icon is unlikely to join UNESCO’s “in danger list”.

Although the overall health of the Great Barrier Reef is still poor, the federal government says recent improvements in water quality should ensure it stays off UNESCO’s in danger list.

The government’s report card for 2012/13 shows marine conditions along the vast majority of coastline adjacent to the reef remain poor despite reductions in key pollutants including sediments, nitrogen and pesticides.

But Federal Environment Minister Greg Hunt is confident UNESCO won’t list the reef as a world heritage site “in danger” because of improvements to water quality from reduced agricultural run-off.

“I don’t expect that will happen,” Mr Hunt told reporters in Brisbane.

“We are likely to be successful … because the facts speak to that.

“The reef is now on the pathway to long-term improvement.”

Queensland Environment Minister Andrew Powell will take the report to a meeting with UNESCO in Qatar this month.

Mr Powell is also confident the reef won’t be rated in danger, but has conceded the overall health of the world icon needs improvement.

“The outlook in this report still suggests that it’s poor and that is consistent with the fact we’ve had many decades now of natural disasters, but also agricultural practices and run-off,” he said.

But green and environmental groups aren’t persuaded the report card will sway the United Nation’s environment arm.

“UNESCO won’t be fooled, they’re concerned specifically about industrialisation of the reef,” Australian Greens Senator Larissa Waters said.

“Despite welcome gains in reducing agricultural run-off, the reef’s inshore water quality remains poor, which will only get worse with mass dredging and dumping planned for the reef’s coastline.”

Australian Marine Conservation Society spokeswoman Felicity Wishart agreed dredging and dumping were ruining the reef.

“You only have to look at the environmental disaster that has occurred at Gladstone which experienced toxic turtles, sick fish and a collapse of the fishing industry following dredging,” she said.

UNESCO made seven recommendations for improving management of the reef last year but a joint AMCS and WWF Australia analysis of federal and Queensland government actions since then says they don’t stack up against the recommendations.

WWF-Australia chief executive Dermot O’Gorman says the federal decision to allow the dumping of three million cubic metres of dredge spoil off Abbot Point means it has failed its international responsibility to protect the reef.

Mr Powell said industrialisation wasn’t an issue as the government had ticked off on all of UNESCO’s requirements by preparing a major port strategy and completing independent reviews of Gladstone harbour.

The federal and state governments also signed a reef trust agreement on Thursday, which Mr Hunt says will ensure the reef’s long-term protection.

The first investments include $5 million for dugong and turtle protection, $5 million to improve water quality from run-off and $2 million for crown-of-thorns starfish control.