Seven public acute hospitals have received letters from HIQA, warning of poor hygiene practices.
The Health Information and Quality Authority found problems with environment and facilities management, hand hygiene, communicable disease control and unclean patient equipment.
It carried out inspections at 49 of 50 public acute hospitals between February 2014 and January of this year, and found that all hospitals could do more to improve hand hygiene and environmental cleanliness.
The report found a need for better internal checks on hand hygiene practice in some hospitals. It also called for greater awareness of when hand hygiene is required moving between "patient zones" and the more general "healthcare area".
HIQA’s Acting Director of Regulation Mary Dunnion said: “Patients have the right to expect that equipment used as part of their care is clean in the first instance and cleaned after use when it is shared with other patients.
"Hospital management need to tackle the problems head on by prioritising environmental cleaning and maintenance in patient areas, and by supporting and ensuring staff compliance with hand hygiene training and implementation. "