Inland communities face the threat of severe flooding with torrential rainfall having left major rivers including the Shannon, Lee, Blackwater, Suir and Nore swollen to breaking point.
Met Eireann has warned that heavy rainfall is expected to last until next week with the Government's emergency watchdog admitting the flood threat will now move from coastal to riverside communities.
Cork – devastated by floods on Monday and Tuesday – is now on flood alert again for the weekend with further high tides forecast.
An estimated €25m worth of damage was caused in Cork and Limerick cities in the space of just 36 hours while in Kerry a cemetery was hit by flash-floods.
River flooding has now replaced coastal flooding as the major concern for Ireland's National Emergency Co-ordination Group (NECG).
"It has been raining pretty much for the last two months and while the threat of coastal flooding has subsided, we are concerned about further threats that exist," NECG chairman Sean Hogan warned.
The Office of Public Works (OPW) said the Shannon, which devastated Limerick last weekend, was "a particular source of concern".
Local authorities in the Shannon basin are monitoring the river on an hourly basis with Athlone having already implemented its emergency flood plan.
Town Clerk Pat Keating confirmed sandbags are now being delivered to critical areas.
However, all Irish rivers including the Lee and Suir are being closely monitored.
Met Eireann warned further heavy rainfall was on the way.
"If we look at what has happened in the last two months . . . we have had a very wet and windy period," forecaster Gerard Fleming said.
"Rivers have become very high in the last couple of months. The OPW and local authorities tell us the rivers are very high and we do foresee very little change in the next few days."
Environment Minister Phil Hogan confirmed that emergency relief payments to flood-hit households have already been made but he said other aid payments will take "a matter of weeks" to organise.
"Local authority staff are going house-to-house in the affected areas to carry out an assessment on behalf of the Department of the Environment, which will form part of the submission I will make next Tuesday," he said.
"Emergency aid is payable immediately . . . I hope that the assessments can be carried out quickly, we can get repairs under way and then we will be in a position to pay."
In Kerry, Kilbanivane Cemetery in Castleisland has been hit by flash floods three times in six weeks.
In Cork, storms ripped away a coastal road at Summercove just 1km from Kinsale.
Bulman Pub owner Pearse O'Sullivan said people were awe-struck by the power of the sea as it demolished the road.
"The huge waves were just rolling in," he said.
In Limerick, the ESB insisted that its Ardnacrusha hydroelectric dam and Parteen Weir had nothing to do with the disastrous city flooding on Saturday.
"ESB has been continuously releasing water at Parteen Weir since Christmas Day. ESB made no sudden changes to its discharge at Parteen Weir last week," the ESB said.
OPW Minister Brian Hayes will tour flood-hit Cork and Kerry today. Tomorrow he will attend a special flood risk-management conference in Cork.
Cork Business Association official Claire Nash, whose restaurant was destroyed in Tuesday night's storm surge, warned that the city cannot sustain further flood damage.
"We've had bad floods in Cork in 2004, 2009 and now three times already in 2014. We just cannot allow this situation to continue," she warned.
The Cabinet will consider a detailed NECG report next Tuesday and proposed increases to flood-prevention programmes.
A €25m aid scheme has been created for flood victims and Ireland is to press for an enhanced aid allocation under the European Solidarity Fund.
Paul Melia and Ralph Riegel