A scientific panel report released last month could not find a cause of the disease outbreak but blamed local flooding as one of the factors, reports ABCNews.
Environment Minister Vicky Darling told State Parliament the new investigation will examine the aquatic ecosystem in the harbour.
"We've established an integrated, aquatic investigation program for Gladstone Harbour to further build on the detailed work already undertaken by this Government and the Gladstone Fish Health Advisory panel," she said.
"This programme will search for possible causes for the fish health issues."
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