ABCNews reports that the Department of Environment and Resource Management imposed a local fishing ban when sick fish were found in Gladstone Harbour in recent months.
Barramundi and other fish turned up with cloudy eyes and discolouration, and the ban forced a number of commercial fishing operators out of business.
Now local fisherman Chris Sipp says he has found 15 dead barramundi in the upper Boyne River in recent days.
"There was one there that had a very severe lesion and the other one definitely had the red infection disease with the pop eye," he told ABC News.
"Probably about six or seven were deteriorated pretty bad."
Many blame a large-scale dredging operation, but the Queensland Government pins the blame on last summer's floods.
Acting Queensland Premier Andrew Fraser says it is difficult to link the two incidents. He says the fish Mr Sipp found had been dead for a couple of days and tests to determine their cause of death have been inconclusive.
"We're talking here about a site that's 12 kilometres upstream," Mr Fraser said.
"Anyone who wants to rush to judgment about linking this to activities relating to dredging of course needs to observe that plain geographical fact in the first place.
"The geography here shows that this is an incident which on first assessments appears to be isolated and not connected to other broader issues."
The Queensland Greens say Gladstone Ports Corporation data shows turbidity levels in the harbour were above normal for four days over the Christmas period.
While it is not linking the latest fish kill to the harbour, the party wants the corporation to have stricter reporting conditions.
Mr Fraser said the Greens were having "a bet each way" by not accepting the work underlying the dredging's environmental approvals.
"If it's good enough to accept the science on climate change then it's good enough to observe the science on issues around Gladstone Harbour," he said.
Gladstone Ports Corporation has approvals to dredge 46 million cubic metres from the harbour in order to expand for gas exports.
It wants the Great Barrier Reef World Heritage area to be redrawn to exclude the harbour.
Mr Fraser expects an independent scientific panel's report on the harbour's sick fish - expected to be released last month - will be available to the Government and the public within a week.
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