The IFA and an Oireachtas committee have both called for the Office of Public Works (OPW) to be given charge of maintaining water levels on the Shannon.
In talks with Minister Brian Hayes, who has responsibility for the OPW, an IFA delegation insisted that it was time for the state body to take the lead role in managing the river.
This position was supported in a special report on recent flooding in the Shannon Basin compiled by the Joint Oireachtas Committee on Environment, Culture and the Gaeltacht.
Among the recommendations set out in the report were to:
1.Give the OPW authority to operate as the lead agency in monitoring and managing flood risk on the Shannon;
2.Monitor water flow on the river and remove any blockages, including silt, that may inhibit the river's flow and cause flooding;
3.Implement an immediate review of the statutory and operational water levels on the Shannon. Maintain waters at a level that facilitates all users, including farmers, commercial interests and ecological and environmental groups;
4.Put a flood early warning system in place;
5.Utilise bogland along the river as a potential flood plain.
Up to 100,000ac in counties Galway, Roscommon, Longford, Westmeath and Offaly have been flooded since early June. The floods have destroyed crops of silage and hay and left thousands of farmers without fodder for the winter.
Speaking after a meeting with Minister Hayes last week, IFA president John Bryan said the minister must address water levels on the River Shannon immediately to avoid further losses for farmers.
"The current system, which is underpinned by protocols dating back to the early 1970s, disregards landowers' interests.
"It is outdated and needs to be overhauled urgently to address the concerns of farmers whose land is submerged in water frequently," Mr Bryan said.
The IFA president said the promise of a lead agency for the river must be delivered upon.
He said the current situation whereby over half a dozen agencies have a say in water levels, with some having a veto on whether remedial works go ahead, is untenable and must be changed.
"Minister Hayes must take a lead here and insist on implementing a strategy. This must include an early warning system for extreme weather patterns and allow water to move on when heavy rainfall occurs.
"We also need to see essential maintenance work carried out.
"All of these measures have to be given legislative effect."