Homeowners are likely to escape paying water charges if there is a problem with their supply that makes the water unsafe to drink.
The Government has retained the right to issue directions to Irish Water and independent regulator, the Commission for Energy Regulation (CER), in the event of problems with the supply such as infection with cryptosporidium or other dangerous bugs.
The relevant minister will have the power to order Irish Water to waive charges in cases where homes are put on 'boil water' notice.
Irish Water takes control of the water network from today and there have been concerns that customers would not be safeguarded in the event of problems with quality.
However, the Department of the Environment said that the minister could issue directions to Irish Water and CER in the event of problems, which could require charges to be waived if the supply was unsafe to drink.
The measure is contained in the Water Services (No 2) Act, which passed through the Houses of the Oireachtas before Christmas.
The Department of the Environment confirmed domestic charges will start from October 1, with households receiving their first bills in January 2015.
Junior minister at the department Fergus O'Dowd said the legislation included "important safeguards" for the public.
"The new act contains a power of ministerial direction to Irish Water or the CER, if required," he said.
"This is a vital safeguard for the public, to ensure they receive a high-quality service and are protected at all times."
Environment Minister Phil Hogan said the transfer of responsibility to Irish Water was a "momentous event". "After extensive work and planning by a range of stakeholders, Irish Water begins work as the national water utility," he said.