All public acute hospitals are being asked to assess their nutrition and hydration capabilities for patients.
It is part of a HIQA review, which will also involve unannounced inspections.
Malnutrition affects more than one in four patients admitted to Irish hospitals and compromises their quality of life.
There are also economic costs associated with the issue - in 2007, it is estimated that €1.4bn was spent on malnourished patients - more than 10% of the healthcare budget that year.
Phelim Quinn, HIQA’s Chief Executive, said: "It has been reported that patients already malnourished on admission are more likely to lose weight during their hospital stay, and their weight loss is proportionately higher. It has a higher incidence in specific patient populations.
"More vulnerable patient populations include older persons, cancer patients, surgical patients and gastrointestinal patients. We believe that these issues form an important barometer of the quality and safety of services and a key indicator of how well the National Standards are understood and implemented."
Inspection teams will visit hospital wards during meal times to see if patients get good quality meals, a choice of food and that they are helped with eating when necessary.
Mr Quinn said: "Initially, hospitals will self-assess their position. The information provided by hospitals in self-assessments will inform the programme of unannounced inspections, which is due to start later this year.
"A national overview of our findings will be published in 2016."