An interim report, by fisheries veterinarian and Sydney University lecturer Matt Landos, says the government has underestimated turtle deaths and failed to conduct proper monitoring in the harbour.
The report was commissioned by the Gladstone Fishing Research Fund and paid for by public donations and fishermen after marine life began falling ill in the harbour.
Australian Greens environment spokeswoman Larissa Waters says the first report to be released by a body other than the Queensland government or Gladstone Ports Corporation (GPC) backs up what the central Queensland town's residents and fishermen have long suspected.
"There is still an ecological crisis in Gladstone harbour," Senator Waters told reporters in Canberra on Wednesday.
"We've still got sick fish, sick crabs, a sick turtle, various different sick sharks.
"There's still something going terribly wrong in Gladstone harbour and yet the Queensland government is still trying to say that everything's fine."
Senator Waters hit out at the federal government for not doing anything to halt the dredging, despite the harbour being in a World Heritage area.
One protester took matters into his own hands on Wednesday to stop the port's dredging work, chaining himself to a dredge in the harbour.
Friends of the Earth activist Mark "Potts" Driscoll's protest coincided with the last day of a visit by a delegation from the United Nations environmental arm UNESCO.
It's here to look at threats to the reef and, based on its recommendations, the World Heritage Committee will decide in June whether to list the reef as a World Heritage Site in Danger.
Friends of the Earth spokesman Drew Hutton said the action was necessary to remind Queensland election voters, ahead of the March 24 poll, of the importance of preserving the Great Barrier Reef.
"The dredging activities in Gladstone are a crime against the environment," Mr Hutton said in a statement.
"The LNG (liquefied natural gas) facilities in Gladstone are another part in the destructive coal seam gas industry in Queensland.
"This industry is destroying our farmland, polluting our water systems, and killing the Great Barrier Reef."
A ports spokeswoman told AAP the protest did not severely impact on or halt operations.
The protest came as a Galaxy Poll, released on Wednesday, showed 91 per cent of Australians oppose federal government plans to charge for the right to dump dredge spoil in the Great Barrier Reef World Heritage Area.
Federal Environment Minister Tony Burke is considering a proposal to charge between $5 and $15 for each cubic metre of spoil disposed of in the marine park.
Mr Burke says some spoils are already dumped within the marine park, but only as a last resort and under strict conditions, and those doing it should have to pay.
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