Members of the Defence Forces have been deployed to Athlone, as well as counties Clare and Limerick, as these areas remain at high risk of further flooding.
Water levels on the River Shannon continue to rise and it has breached its banks in Athlone.
Up to 100 homes in the town are expected to be flooded in the coming days.
Chairman of the National Emergency Co-Ordination Group Sean Hogan said the Shannon is expected to peak at the weekend.
Met Éireann has warned of strong gale force winds on all Irish coasts and on the Irish Sea overnight.
Westmeath County Council activated its flood emergency response plan and brought in the civil defence and the Army to assist homeowners whose properties were threatened by flooding.
Thousands of euro in damage also has been caused to shops and businesses further north at Carrick-on-Shannon.
Met Éireann said there will be some respite tomorrow and Friday but further heavy rain is expected across south Munster.
Heavy rain & gusting winds expected, please drive with care esp high sided vehicles,pedestrians xtra care needed @ coastal areas & waterways
— An Garda Síochána (@GardaTraffic) December 9, 2015
Two sections of 15 troops and two military vehicles were deployed at Clonlara in Co Clare following a dramatic rise in water levels downstream of Parteen Weir on the River Shannon.
30 troops and four vehicles were deployed at Castleconnell in Co Limerick, 12 troops and two vehicles assisted efforts in Ballinasloe, Co Galway, and 35 troops and four vehicles went to Athlone.
A number of properties in the Springfield area of Clonlara in southeast Clare have been flooded, with army personnel assisting with sandbagging in an effort to stem the floods.
ESB Networks said: "The heavy rain last weekend has increased water inflows significantly into the Lee Dam reservoirs at Inniscarra and Carrigadrohid.
"On Monday, ESB increased its discharge from 150 to 180 cumecs (cubic metres per second) from Inniscarra Dam.
"We expect to continue to spill at Inniscarra Dam over the coming week to draw down reservoir levels.
"There may be associated flooding of roads, land and property adjacent to the banks of the River Lee downstream of Inniscarra.
"We continue to closely monitor the situation and are in communication with the local authorities and response agencies in accordance with our normal operating procedures," the ESB added.
The ESB has warned that it may have to increase the flow of water from the Parteen Weir again.
Pumping... pic.twitter.com/yeFu9jdPt8
— Pat McGrath (@patmcgrath) December 9, 2015
Thousands of litres of water have been pumped away from St Michael's Square in Ballinsloe in an ongoing effort to prevent the town from flooding.
Sandbags have been placed at the bottom of the square to stop water from the River Suck from spreading into homes and businesses.
While some properties at the verge of the square have been affected by flooding, locals say the defences have improved the situation since 2009, when large areas of the Co Galway town were underwater.
Water levels have fallen since yesterday but there are concerns about the possible impact further rainfall could have in the coming days.
Meanwhile, a number of roads have been closed in the west including the R280 in Leitrim Village and the R284, R287 and R294 in Sligo.
A spokesperson for Sligo County County Council said: "The worst affected roads are in the Carraroe area due to very high water table and land saturated by persistent, heavy rain.
"Motorists are strongly advised not to attempt to drive through flooded roads as they can cause major damage to their vehicles and can also cause flooding in adjacent houses."
Worst of Shannon flooding yet to come
A District Engineer for Clare County Council has warned that the worst of what is expected in terms of flooding along the Shannon has not yet been seen.
Hugh McGrath said the council is preparing for water levels in the river to rise further and said they have not peaked.
Mr McGrath said he was not in a position to say when water levels may peak, but added they are preparing "for the possibility it could get a lot worse".
The Irish Red Cross has said it will set up emergency drinking water points in three areas along the River Shannon considered at high risk of further flooding.
Bottled water was distributed in Athlone, Portumna and Montpelier in Co Limerick.
A farmer in Co Clare has said the Shannon has never been maintained properly and there is not one body in charge of it.
Páidí Ryan said the ESB, Office of Public Works, Irish Water and the fisheries are all involved in maintaining the river.
Mr Ryan said there is a huge problem in the lower Shannon and he believed that if the river was cleaned down at the mouth it would solve many problems.
However, he said the problem will never be resolved until one body takes responsibility for the river.
Fianna Fáil leader Micheál Martin has called on the Government to introduce a scheme to give insurance cover to flood-risk communities, similar to that in the UK.
During Leader's questions, Mr Martin said a game changer was needed in terms of policy change and it was a key issue for small businesses and farmers.
However, the Taoiseach Enda Kenny said the British scheme of insurance for flood risk areas excluded houses built after 2009 and small businesses.
