It addresses the impact of climate change on seabirds, and obtained by The Australian under freedom of information laws.
According to a report in The Australian, tens of thousands of seabirds are failing to breed because warmer water from more frequent and intense El Nino events means there is insufficient food to raise their young.
Warm water near the surface forces fish, plankton and other prey into deeper water, where it cannot be reached by seabirds.
"Recent analyses at key sites have revealed significant declines in populations of some of the most common seabird species, which raises concerns regarding the threatening processes acting on these populations," said the report, prepared by C and R Consulting.
The report, 'Seabirds and Shorebirds in the Great Barrier Reef World Heritage Area in a Changing Climate', says that the reef is home to between 1.3 and 1.7million seabirds and half the world's population of several species.
The authors concluded that recent climate fluctuations were having significant detrimental impacts on seabird populations.
In the Coral Sea, populations of great and least frigatebirds declined by 6-7 per cent annually between 1992 and 2004.
Despite a return to more favourable conditions since the severe El Nino event of 1997-98, populations have not recovered.
On Raine Island, in the northern barrier reef, populations of at least 10 of the 14 breeding seabird species have been falling.
Numbers of common noddies have fallen by 96 per cent, sooty terns by 84 per cent, bridled terns by 69 per cent, and red-footed boobies by 68 per cent.
The park authority's vulnerability assessment report said that there is no evidence of significant human interference or habitat loss on Raine Island, indicating "depletion of marine food stocks linked to changing climate" as the cause.
On the Swain Reefs, in the southern reef, the number of brown booby nests has dropped from 350 in 1975 to less than 30 since 2000.
"The declining trend was consistent throughout the region and was not simply a consequence of inter-seasonal migration between islands," the report said.
Negative impacts on seabird populations were recorded in all parts of the barrier reef, in virtually all species, and in nearly all components of reproductive biology.
Timing of breeding, year-to-year recruitment, number of breeding pairs, annual hatching, chick growth and adult survival were all affected.