Approval for the device would have paved the way for the river to re-open for salmon fishing.
IFI director Seán Ryan said: “We are disappointed. The counter was one of a number of tools that could have led to the re-opening of the river. There is no guarantee it would have been re-opened.”
And anglers’ representative Peter Hehir said: “The decision beggars belief. We’re stunned. The IFI staff are stunned. I can’t understand why two Government departments cannot work together instead of fighting each other.”
The river passes through Ennis into the River Shannon. It has been closed to salmon fishing since 2007 and a fish counter is required to determine if salmon fishing stocks have recovered to allow salmon fishing recommence.
Last year Ennis Town Council gave the go-ahead for the plan.
However, this was appealed by the Department of the Environment who expressed concerns over the impact the development would have on sea lamprey spawning grounds in the Special Area of Conservation (SAC).
The IFI told the appeals board it was likely that economic benefits to the region through angling tourism would flow from the fish counter being in use, in the event of the River Fergus being re-opened. The IFI contended that a possible loss of a small proven lamprey spawning area would have a negligible impact considering the access provided for sea lamprey to the greater Fergus catchment of some 600 sq km.
Reacting to the decision, Mr Hehir of Fergus Salmon Anglers said anglers were “bitterly disappointed”.
“We have been fighting for this for five years. The Fergus is one of the best early spring rivers in the country.”
Mr Ryan said that the IFI had looked at other sites along the river for the counter, but they were not very promising.