Superquinn, Lidl and Aldi had to withdraw the bottled water supplied by Shannon Minerals after scientists discovered bacteria in the water which could indicate faecal contamination.
Some customers at the stores bought the products before the supermarkets had withdrawn the items.
The Food Safety Authority of Ireland said in a statement: “Operations at the plant have been suspended until the cause is identified and appropriate remedial action taken.”
Shannon Minerals has stated that a change of guidelines were the reason for the problem, as it was not advised that a change on criteria had taken place.
The company was still using guidelines given by an environmental health officer last October.
Shannon Minerals is a family-owned business in Limerick, which produces spring water, flavoured water and rehydration drinks.