People are afraid to complain about the care and treatment they get in hospitals because they are worried what will happen to themselves or their loves ones, according to the Ombudsman.
An investigation by the Office of the Ombudsman also found that people do not complain as they do not believe it would make any difference.
The investigation found many people who use hospital services do not know how to make a complaint and are unaware of the support available to do so.
Complaints to the Ombudsman about healthcare represent 20% of all complaints received.
This is very low compared with Northern Ireland (over 60%) and the UK Parliamentary and Health Services Ombudsman (80%).
Speaking on RTÉ's Morning Ireland, Ombudsman Peter Tyndall said people need to file complaints and make mistakes known, so they do not happen again.
He said: "Our concern was that without people complaining about their health care we were going to see issues within the health service not being addressed."
The 'Learning to Get Better' report is the most extensive investigation carried out by the Office of the Ombudsman.
It involved surveys of all public hospitals, site visits to a sample of hospitals, interviews with front line and senior hospital staff, focus groups with members of the public, consultations with health sector and advocacy groups, and a review of complaints dealt with by some hospitals.
Mr Tyndall said the investigation also found the complaints system is not working properly within the health service and he called on this to be rectified.
He said: "If those complaints aren't reaching offices then they can't be dealt with.
"On the other hand if they are not dealt with properly then the results won't be there.
"We've spelled out how complaints need to be dealt with in the future.
"Hospitals need to welcome complaints, that the leadership in hospitals need to seem to be acting on the findings of the complaints and we've said that patients who complain must be told about what's going to be done and then must be told that it has been done and that it has worked", he said.
The report says multiple methods of making a complaint should be available and easily understood, both during and after treatment, with Complaints Officers within each hospital available to meet complainants.