Taoiseach Bertie Ahern agreed with Fine Gael leader Enda Kenny that hospitals were cleaner when religious orders were in charge.
Mr Kenny said the "difference between the days of matrons running hospitals, and the hospital management system that exists now, is that standards of hygiene in many hospitals now are lower and this is reflected in the findings of the third report today".
Mr Ahern said: "I agree with Deputy Kenny's comments on the superiority of the old system of matrons and religious orders and I worked under such a regime. They moved heaven and earth in the wards to ensure that hygiene prevailed and my generation remembers the smell associated with hospital hygiene. That is no longer evident today."
Replying to questions on the hospital hygiene report, Mr Ahern said notice had been served to corporate management in hospitals to make hygiene a high priority in the future.
He said it was the first national hygiene services quality review report from the Health Information and Quality Authority (Hiqa), the new agency the Government promised.
The report could not be compared with the previous ones because it was carried out on a different basis. "The report is part of an important new development in the Irish health service that will see standards set, monitored and reported on objectively," Mr Ahern said.
"It gives the results of the review conducted in the 51 acute hospitals between March and September. While hospitals generally performed well in the areas of hygiene and in-service delivery, the results on governance were poor - that aspect was not included in previous reports.
"This contributed to disappointing overall results. While improvements have been made and are acknowledged in the report, no hospital received a very good rating."
He said the method of assessment and the criteria used in the latest report were substantially different and, rightly, more onerous than those in previous audits carried out by the Health Service Executive, and the results, therefore were not comparable.
Previous audits concentrated only on service delivery.
Mr Ahern said the report also sought to "to see contractors in hospitals abiding by far higher standards - they are, frankly, being paid enough and should abide by the standards set by Hiqa".
