Drinking water supplies to 6,000 homes and business in Co Galway have been contaminated by human and animal waste.
Galway County Council says the situation is very serious and engineering teams are working around the clock to try to eliminate the contamination. It has issued boil water notices for two areas in the county.
A boil notice has also been issued for more than 500 homes in counties Limerick and Clare.
The notice was put in place following consultations between the local councils and the HSE.
Limerick County Council's water services section detected a deterioration in water quality in the Montpelier Water Supply Scheme.
It serves Montpelier in Co Limerick and the Clare villages of O'Briensbridge and Bridgetown.
Applications forms and information about the Government's Humanitarian Assistance Scheme for those households affected by floods have been published on the Department of Social and Family Affairs' website.
Click here for further information.
Elsewhere, the Financial Services Ombudsman has said he hopes that insurance companies will not rely on legal opt-outs and loopholes when dealing with the claims of people affected by the floods.
Joe Meade said their claims should be treated with care and attention and the insurance industry should take account of the unusual circumstances that have arisen.
He advised anyone who feels their claim has not being treated properly to contact his office, which will investigate the complaint.
Minister of State Martin Mansergh has said that the flood relief fund will cover damage to homes, including carpets, bedding and furniture, and that structural damage may also be covered.
However, Mr Mansergh said assistance would not be given where a loss is covered by an insurance policy.
The Dept of Social And Family Affairs has said that financial help will be given to flood victims through Community Welfare Officers for normal household appliances - but not for luxury items.
Brian O'Raghallaigh for the Department, told the Oireachtas Environment Committee they would also assist with damage to an owner-occupied home and with medical treatment where there was no insurance policy.
Meanwhile, heavy rain in the west have raised concerns of renewed flooding.
Flooding between Ballinasloe and Portumna is said to be easing slightly, but there is fresh concern about rising water levels near the village of Ardrahan in south Galway.
Elsewhere, flood levels in the Waterways Estate in Sallins, Co Kildare have fallen by about a foot, following a pumping-out operation that began last night.
However, the estate is still submerged and it will be later in the week before residents who live in higher storey homes will be able to return.
Meanwhile, the water levels on Lough Ree on the River Shannon have fallen by 6cm overnight. The level above Athlone Lock also fell by 5cm overnight also.
In total Lough Ree has dropped by 8cm since Saturday with a similar fall in levels recorded in Athlone for that period.
According to figures from Waterways Ireland, Lough Allen has dropped by 11cm in the past 24 hours - yesterday the lake fell by 24cm.
The ESB says it will increase the discharge rate from Poulaphouca Reservoir today, but it does not expect it to impact on water levels on the River Liffey.
Cork water mostly restored
Engineers from Cork City Council have restored water to most of the 18,000 homes, which had been without service for over a week as a result of the flooding of the Lee Road water treatment plant.
However, several hundred homes, businesses and a school are still without supplies at Ballinlough on the south-east side of the city.
The City Council said it hopes to have the service restored there today.
A boil notice remains in place to the north of the north channel of the River Lee in the city and testing on the quality of the water there is continuing.
The council is treating the aftermath of the flooding in the city as a civic emergency and it said that status will remain water supplies have been restored to all areas.