Flooding has hit train services between Limerick and Galway as waters have risen above the rail at Kiltartan, Co Galway.
Services are to be be part-substituted by bus for a number of days.
Irish Rail said following a precautionary suspension of trains on Tuesday morning, an inspection revealed that water levels have risen to 200mm above the rail and are continuing to rise.
Bus transfers will be operation on Tuesday morning between Gort and Athenry, and also between Ennis or Gort and Athenry for afternoon and evening services.
Irish Rail said based on the continuing rise in water levels, and past experience the company believes the line will remain closed “for a number of days”.
Meanwhile in Athlone, Co Westmeath, fire brigade units were on duty all night attempting to keep water pumped away from housing areas, Minister of State for the Office of Public Works has said.
Kevin ‘Boxer’ Moran said water levels rose two inches on Monday night and that land in the area has been saturated since last October.
Over eight inches of rain has fallen in the past three weeks causing flooding along the River Shannon, particularly in Carrick-on-Shannon and around Athlone and Cloonlara, Co Clare.
"Conditions are a small bit better today with showers rather than rainfall forecast, but more rain is due on Saturday. There is talk of bringing in the army to help," Mr Moran told RTÉ's Morning Ireland on Tuesday.
“When the media frenzy dies down people will still be facing this for the next six to eight weeks.”
Taoiseach Leo Varadkar and Mr Moran were met by irate residents and farmers during a visit to Athlone on Monday to see the extent of the flooding there.
Mr Varadkar said the Government had committed to invest €1 billion in flood defences and 98 different projects were underway around the State. He said this work would become more necessary in the future.
Local residents told Mr Varadkar and the Minister that they were in the same situation as in late 2015 and 2009, when their lands and homes suffered water damage.
The Taoiseach said the Defence Forces would be deployed in the coming days, especially in cut-off rural areas.
Horse trainer Tom Cleary, based just outside Athlone, spoke about the efforts to keep his stables clear of flood water and to ensure the horses are safe.
“There’s not a lot we can do but move the animals to safety. There are some good people out there offering to take them,” he said.
“Most of the stables can be saved, but we need pumps which we have ordered, but we are still waiting for them from the council.
“It’s a bit worse this morning, there’s two inches more [of water] and four stables are now affected.”
Mr Cleary said local TDs Robert Troy (Fianna Fail) and Peter Burke (Fine Gael) had been in repeated contact with him and the council who had promised that pumps would be provided, but have yet to arrive.
“Nobody appeared, but I understand they must be very busy,” he added.
Geraldine Mason, from Co Clare, said the fire brigade had kept pumps going all night, ensuring her home was dry on Tuesday morning. Ms Mason said she shed tears of relief this morning as she has no home insurance.
Tim Cullinan, president of the Irish Farmers' Association (IFA) said the Government must take "urgent action" given recent heavy rain and flooding on farmland.
“We need an immediate assessment of damage to determine losses and a financial aid package. The fact that insufficient action has been taken to manage the River Shannon is a contributory factor in the current flooding crisis,” he said.
“I met farmers in Longford in the last week and they raised the problem of the levels in the River Shannon. With better monitoring, we could avoid some of the problems we have now. We need real action to protect farmers and other members of these communities.”