Minister for Health Mary Harney has visited meat factories where standards of hygiene were higher than they were in hospitals, she told the Dáil.
"We would not allow food to be produced in the kind of hygiene environment in which patients are treated," she said, as she promised that the results of a hygiene audit of each hospital in the State would be made public.
"There is no excuse for low standards when huge money is being spent on cleaning programmes involving both in-house cleaning and outside contracts," she said.
Responding during Question Time to Opposition concerns about the growing incidence of the MRSA - or the hospital "superbug" - she confirmed there were 553 cases last year and 145 cases for the first three months of this year.
Fine Gael health spokesman Dr Liam Twomey warned that at least 200 MRSA cases would be coming to court in the foreseeable future. The issue was becoming "another litigation nightmare in respect of the health care services because simple protocols have not been followed since 1995".
He said levels of septicaemia were a good indicator of how out of control MRSA was in a hospital. "Publishing those figures for each hospital would provide a ready answer as to where the problem lies," he said.
Dr Twomey also pointed out that a meat factory or a hotel was raided by environmental health officers but a hospital was not, and he called for the establishment of a "flying squad of experts" who would "raid hospitals, which should be the safest places in the country".
Ms Harney said there was merit in such a hit squad "but unless the squad were to do the cleaning, it would not achieve much".
Labour's spokeswoman Liz McManus pointed to the "terrible irony in the fact that teams are sent into workplaces to check whether somebody is puffing a cigarette while MRSA is rampant through the hospital sector. Collecting data and carrying out surveillance does not ensure action on this terrible infection."
She asked would the Government fight every legal action taken against it.
"I presume that if litigation arises it will involve the institutions concerned, namely hospitals which have their own insurance policies," Ms Harney replied.
John Gormley, Green Party spokesman, said that "hygiene simply does not exist in some of our hospitals".
He added that "in the old days, when we had no money and no Celtic Tiger, our hospitals were spotless. Now that we have the money we have private companies in - more privatisation which the Tánaiste favours - and many hospitals are filthy."
Ms Harney said "if companies are being paid to perform a cleaning job and are not doing it, other companies will have to be found".
