The Great Barrier Reef Marine Park Authority (GBRMPA) says it addressed concerns raised about a large marina development near the reef.
The ABC has obtained documents that show the authority identified serious reef health concerns in relation to the project, which it later approved.
The marina is part of a $600 million eco-tourism resort on Great Keppel Island off Rockhampton.
In a statement on Monday, GBRMPA said an email sent to resort proponent GKI Resort Limited in February last year raised concerns about a sewage pipeline.
Those concerns related to potential impacts on water quality and coral.
The firm responded later that month that its designs had been modified and no longer included the pipeline, so a permit wasn’t issued for that aspect of the project.
Two other permits were issued though, giving permission to build a water, power and phone pipeline and a marina.
“Both of these permits were approved with strict conditions to help protect biodiversity, heritage and social values of the marine park,” a GBRMPA spokeswoman said.
“Any remaining risks were addressed.”
Documents obtained by the ABC reportedly show GBRMPA officers raised a raft of concerns about the potential for reef harm in relation to the proposed sewage pipeline.
They were also concerned the environmental impact statement provided by GKI Resort Limited was often contradictory, vague or missing key information.
The Queensland and federal governments approved the resort but it was up to the GBRMPA to grant permits for the marina project as it required dredging.
Greens Senator Larissa Waters has said she is worried the authority has come under political pressure to approve developments that may harm the reef.
A spokesman for federal Environment Minister Greg Hunt said the authority was completely independent.
The spokesman said the previous Labor government approved the Great Keppel Island project “according to national environment law”.