Canberra released a five-yearly review of the reef and moves to protect it, to address concerns raised by UNESCO and persuade the world body not to put the key tourist attraction on its "in danger" list next year.
"Even with the recent management initiatives to reduce threats and improve resilience, the overall outlook for the Great Barrier Reef is poor, has worsened since 2009 and is expected to further deteriorate," the government said in its outlook report.
The fragile reef, which stretches 2,300km along Australia's east coast, is the centrepiece of a campaign by green groups and marine tourist operators aiming to stop a planned coal-port expansion that would require millions of cubic metres of sand to be dredged up and dumped near the reef.
The reef has the world's largest collection of coral reefs, with 400 types of coral, 1,500 species of fish, 4,000 types of mollusc, and is home to threatened species, including the dugong and large green turtle, the World Heritage list says.
The government said runoff from farms, crown-of-thorns starfish and climate change remain the biggest threats to the reef, but acknowledged that shipping and dredging occur in reef areas already facing pressure from other impacts.
"Greater reductions of all threats at all levels, reef-wide, regional and local, are required to prevent the projected declines in the Great Barrier Reef and to improve its capacity to recover," the government said.
The government said it would not allow any port development outside long-established ports in Queensland. Those existing ports include Abbot Point, where India's Adani Group and compatriot GVK plan a huge coal terminal expansion, and Gladstone, where ship traffic is set to increase sharply from 2015 as huge new liquefied natural gas plants start exports.
Green groups said the report did not let off the hook the mining industry, which is digging up coal for export, adding to climate change and expanding ports along the reef.
"The greatest risk, again, is climate change," said Wendy Tubman, an official of the North Queensland Conservation Council, which is leading a legal fight against the Abbot Point expansion.
"And we all know what the greatest contribution to climate change is: that's mining coal for export."
The Queensland Resources Council, which represents the mining industry, said it supported the effort of the state government to improve port development and management along the reef.
At a meeting in Doha in June, the World Heritage Committee of UNESCO deferred until next year a decision on whether to place the 300,000-sq-km reef on its list of sites in danger.
The United Nations Educational, Scientific and Cultural Organisation is concerned over the proposed coastal developments, and has asked Australia to submit an updated report on the state of conservation of the reef, which sprawls over an area half the size of Texas, by next Feb 1.