Failure to come up with a satisfactory plan could result in the site being placed on the "in danger" list, the committee said during its 37th session in Phnom Penh, Cambodia.
Although Australia has made some progress, "some issues still need to be addressed more forcefully," Marc Patry, programme specialist at the UNESCO World Heritage Centre, told dpa.
The situation is "complicated," he said, and the natural resources in the area are an "obstacle" to its conservation, Patry said.
By 2014, Australia has to improve water quality monitoring and limit port development to existing port areas, according to the World Heritage Committee.
Patry added that an "in danger" listing should not be seen as punishment, but as a tool to increase public support for conservation.
The site encompasses the world's largest coral reef. The more than 3,000 individual reef systems and coral cays, and hundreds of tropical islands, contain an abundance of marine life.
Among the 38 World Heritage sites currently listed as "in danger" are the Everglades National park in Florida and the Old City of Jerusalem.
The 21-member committee is to debate the status of 30 cultural and natural sites, including the Mount Etna volcano in Italy, until Sunday.