Environment Minister Greg Hunt has ordered an inquiry into the Great Barrier marine authority.

Federal Environment Minister Greg Hunt. Photo: Andrew Meares

Australia has argued it is making substantial progress on United Nations requests for better protection of the Great Barrier Reef and it should not be listed among world heritage sites ''in danger''.

In a progress report to the UN World Heritage Committee, the federal and Queensland governments say the natural values the reef was protected for are still largely intact, although in parts - such as inshore areas south of Cooktown - they are declining.

The report was delivered to the UN on Saturday, a day after final approval was granted to dump in the reef's water 3 million cubic metres of dredging sludge from the expansion of coal export terminals at Abbot Point.

The World Heritage Committee has threatened to put the reef on a list of world heritage sites considered ''in danger'' after it became concerned in 2012 over the impact of the numerous resource projects slated for the reef's coast.

Australia needs to show significant progress on UN recommendations for better reef management to avoid a downlisting. Tourism operators have warned an ''in danger'' listing would damage their businesses.

In their report the governments point to programs aimed at reducing threats, including development of a 2050 sustainability strategy, water quality measures and a draft Queensland ports strategy.

Environment Minister Greg Hunt told Fairfax Media there was genuine improvement in key reef indicators in regards to dugongs, turtles, seagrass and coral. He said the Coalition had also rejected what he described as Labor's multiple new port strategy, and was containing development to five existing port areas.

''Early indications are that these are important and well received developments internationally,'' he said.

''It is a permanent task for every Australian government to protect and maintain the reef; nobody can ever rest on that. But there should be no way the reef can and should be considered 'in danger'.''

Australian Coral Reef Society president, Professor Peter Mumby, said many argued convincingly that the reef was in the worst shape since monitoring began. He said the progress report played down industrial development threats. Development already on the table, he said, would add 14 million tonnes a year of damaging sediment to reef waters.

''We have real concerns over development that have not been addressed,'' he said.

University of Queensland coral reef ecologist, Dr Selina Ward, said the Abbot Point decision was dangerous because the best modelling showed dumped sediment would drift to outer areas, hurting coral and seagrass.

The government progress report said extreme weather events and climate change were the biggest threats to the reef. It also pointed to nutrient and sediment run-off from land clearing and agriculture, and associated crown-of-thorns outbreaks.

It said pollution from other sources, including port development and dredging, ''is minor but may be highly significant locally and over short time periods''.