The case involves around 60 claimants who are seeking compensation from the Gladstone Ports Corporation, blaming an outbreak of diseased fish last year on the dredging programme in the harbour, reports ABCRural.
Government studies say the problem has been caused by natural events, including floods.
The court has rejected an application to hear a A$20 million class action, but lawyers representing commercial fishers say they'll continue to fight for compensation in other jurisdictions. Commercial fishermen Trevor Falzon says today's decision is not the end of the line.
"While it was a setback to us, we can just move forward from here. I am going to show everybody that the fish in the harbour are not safe to eat."
The Gladstone Ports Corporation says it has always been ready to offer compensation to fishermen affected by loss of access, but says scientific studies do not support the theory dredging is to blame for diseased fish.
Ports Corporation CEO Leo Zussino says the fishermen will receive compensation as soon as possible.
"The corporation will certainly work very closely with the Queensland Government to start offering compensation as was determined by the judge to the appropriate, eligible commercial fish operators."