A major assessment of the Great Barrier Reef singles out climate change as its greatest threat.

The Great Barrier Reef remains under significant threat.

Climate change is the most serious issue it faces, a federal government report says, with fears of “far reaching consequences in the decades to come”.

Coastal development, poor water quality from land-based run-off and fishing continue to threaten Queensland’s underwater marvel, the 2014 Great Barrier Reef Outlook Report and Strategic Assessment found.

Key habitats in the central and southern inshore regions have continued to deteriorate despite some progress during the past five years.

But federal Environment Minister Greg Hunt highlighted increases in the populations of humpback whales and loggerhead turtles.

He also welcomed the report’s finding that nutrient, sediment and pesticide loads entering the ecosystem had decreased.

“These are important milestones for the long-term protection of this global icon,” Mr Hunt said in a statement.

However, dugong populations have continued to decline.

Conservation groups believe state and federal environment ministers have failed to act fast enough to prevent the health of the reef from getting worse.

Australian Marine Conservation Society campaigner Felicity Wishart called for an immediate stop to industrial dredging and dumping.

“We know that ministers have within their powers the ability to stop things like dredging and dumping in the reef, they’re just choosing not to do it,” she told AAP, adding planned dredging between between Cairns and Gladstone could see more than 22 million cubic metres dumped in the reef’s waters.

While the report found that the effects of port activities upon the reef are significant, “they are relatively more localised than the broadscale impacts from land-based run-off”.

The World Heritage Committee is assessing whether the reef should be classed as a World Heritage site in danger.

UNESCO’s annual meeting in June chose to give Australia until February next year to show that it is looking after the health of the reef.