Significant investment is needed to protect farmers living near rivers and coasts from flooding, the Irish Farmers Association (IFA) president said.
The total flood damage bill across the country has been reportedly estimated at €100 million so far by local authorities.
Eddie Downey visited farms along the River Shannon today.
"In the longer term, a significant investment programme would be needed to alleviate the pressure on farmers living near rivers and coastal areas," he said.
He added the recent storm and flood damage that has wreaked havoc on many coastal and river catchment areas must be fully assessed by Government and support given.
He said agriculture development authority Teagasc should immediately assess the damage to farm viability in the worst affected areas and produce proposals to assist affected families.
The IFA warned this month that thousands of acres of prime farmland had been left under water, with farmers facing the threat of even more severe river flooding in the coming weeks.
Those in counties Galway and Clare and in the Shannon, Lee, Blackwater, Suir, Barrow and Slaney river basins have been amongst the hardest hit by storms and floods since January 1.
This month stretches of the Shannon were six feet (182cm) higher than the normal summer-time navigational level, it was claimed, while the high water mark was seven inches (18cm) higher than the previous highest tide in the city.
Cork, Waterford, New Ross and parts of county Galway, Clare and Kerry were among the areas worst hit by widespread flooding.
Among damage done by heavy rain and the seas were floods in the Mall in Waterford with the city's train station also closed. Dungarvan was also affected.
In Cork, flood waters were as high as three feet (91cm) in some places. They receded as the day went on but homes and businesses in the city centre were again left counting the cost.
A combination of high tides, rain and strong winds were blamed for both channels of the River Lee bursting its banks.
The rail line between Cork and Cobh and Midleton was also closed for a time due to the weather, while ferry sailings between Passage East and Ballyhack were also disrupted.
In New Ross, the bridge was impassable and the quays were closed to traffic because of flooding.
The National Directorate For Fire & Emergency Management, Department of the Environment, received no reports of major episodes of flooding overnight.
A spokesman for the organisation said Met Eireann has advised that the current threat of stormy weather from Wednesday onwards remains in place and the rainfall will serve to top up the already near capacity of rivers and still poses a major risk.
"This risk is heightened in slow moving rivers and particularly the Shannon. The Barrow, Nore, Suir Slaney, Lee and Blackwater are also at very high levels and any additional rain can cause serious flooding," he said.